RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4072
(191 letters)
>gnl|CDD|188752 cd09366, LIM1_Isl, The first LIM domain of Isl, a member of LHX
protein family. The first LIM domain of Isl: Isl is a
member of LHX protein family, which features two tandem
N-terminal LIM domains and a C-terminal DNA binding
homeodomain. Isl1 and Isl2 are the two conserved
members of this family. Proteins in this group are
found in the nucleus and act as transcription factors
or cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs, such as
the pituitary gland and the pancreas. Isl-1 is one of
the LHX proteins isolated originally by virtue of its
ability to bind DNA sequences from the 5'-flanking
region of the rat insulin gene in pancreatic
insulin-producing cells. Mice deficient in Isl-1 fail
to form the dorsal exocrine pancreas and islet cells
fail to differentiate. On the other hand, Isl-1 takes
part in the pituitary development by activating the
gonadotropin-releasing hormone receptor gene together
with LHX3 and steroidogenic factor 1. Mouse Is l2 is
expressed in the retinal ganglion cells and the
developing spinal cord where it plays a role in motor
neuron development. Same as Isl1, Isl2 may also be able
to bind to the insulin gene enhancer to promote gene
activation. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 55
Score = 109 bits (275), Expect = 4e-32
Identities = 50/55 (90%), Positives = 53/55 (96%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
CVGCGG+IHDQYILRVAPDLEWHAACL+CAEC Q+LDE CTCFVRDGKTYCKRDY
Sbjct: 1 CVGCGGKIHDQYILRVAPDLEWHAACLKCAECGQYLDETCTCFVRDGKTYCKRDY 55
>gnl|CDD|188760 cd09374, LIM2_Isl, The second LIM domain of Isl, a member of LHX
protein family. The second LIM domain of Isl: Isl is a
member of LHX protein family, which features two tandem
N-terminal LIM domains and a C-terminal DNA binding
homeodomain. Isl1 and Isl2 are the two conserved members
of this family. Proteins in this group are found in the
nucleus and act as transcription factors or cofactors.
LHX proteins are critical for the development of
specialized cells in multiple tissue types, including
the nervous system, skeletal muscle, the heart, the
kidneys, and endocrine organs, such as the pituitary
gland and the pancreas. Isl-1 is one of the LHX proteins
isolated originally by virtue of its ability to bind DNA
sequences from the 5'-flanking region of the rat insulin
gene in pancreatic insulin-producing cells. Mice
deficient in Isl-1 fail to form the dorsal exocrine
pancreas and islet cells fail to differentiate. On the
other hand, Isl-1 takes part in the pituitary
development by activating the gonadotropin-releasing
hormone receptor gene together with LHX3 and
steroidogenic factor 1. Mouse Isl2 is expressed in the
retinal ganglion cells and the developing spinal cord
where it plays a role in motor neuron development. Same
as Isl1, Isl2 may also be able to bind to the insulin
gene enhancer to promote gene activation. All LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 55
Score = 92.1 bits (229), Expect = 3e-25
Identities = 36/55 (65%), Positives = 44/55 (80%)
Query: 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKDDH 151
C KC +F + DFVMRA+ KIYH++CF C C +QL+PGDEFALR+DGLFCK DH
Sbjct: 1 CAKCQQSFSKNDFVMRARTKIYHIECFRCSACSRQLIPGDEFALRDDGLFCKADH 55
>gnl|CDD|188855 cd09471, LIM2_Isl2, The second LIM domain of Isl2. The second LIM
domain of Isl2: Isl is a member of LHX protein family,
which features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
Isl proteins are found in the nucleus and act as
transcription factors or cofactors. Isl1 and Isl2 are
the two conserved members of this family. Mouse Isl2 is
expressed in the retinal ganglion cells and the
developing spinal cord where it plays a role in motor
neuron development. Isl2 may be able to bind to the
insulin gene enhancer to promote gene activation. All
LIM domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 55
Score = 70.0 bits (171), Expect = 1e-16
Identities = 30/55 (54%), Positives = 39/55 (70%)
Query: 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKDDH 151
C +C L F D VMRA++ +YH++CF C VC +QL+PGDEF LRE L C+ DH
Sbjct: 1 CAQCRLGFSSSDLVMRARDSVYHIECFRCSVCSRQLLPGDEFCLREHELLCRADH 55
>gnl|CDD|188755 cd09369, LIM1_Lhx2_Lhx9, The first LIM domain of Lhx2 and Lhx9
family. The first LIM domain of Lhx2 and Lhx9 family:
Lhx2 and Lhx9 are highly homologous LHX regulatory
proteins. They belong to the LHX protein family, which
features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as
transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
Although Lhx2 and Lhx9 are highly homologous, they
seems to play regulatory roles in different organs. In
animals, Lhx2 plays important roles in eye, cerebral
cortex, limb, the olfactory organs, and erythrocyte
development. Lhx2 gene knockout mice exhibit impaired
patterning of the cortical hem and the telencephalon of
the developing brain, and a lack of development in
olfactory structures. Lhx9 is expressed in several
regions of the developing mouse brain , the spinal
cord, the pancreas, in limb mesenchyme, and in the
urogenital region. Lhx9 plays critical roles in gonad
development. Homozygous mice lacking functional Lhx9
alleles exhibit numerous urogenital defects, such as
gonadal agenesis, infertility, and undetectable levels
of testosterone and estradiol coupled with high FSH
levels. Lhx9 null mice are phenotypically female, even
those that are genotypically male. As in other LIM
domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein.
Length = 54
Score = 64.3 bits (157), Expect = 2e-14
Identities = 28/55 (50%), Positives = 35/55 (63%), Gaps = 1/55 (1%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
C GCG +I D++ L D +WHA+CL+C EC LD +CF RDG YCK DY
Sbjct: 1 CAGCGEKIQDRFYLLAV-DRQWHASCLKCCECRLPLDSELSCFSRDGNIYCKEDY 54
>gnl|CDD|188759 cd09373, LIM1_AWH, The first LIM domain of Arrowhead (AWH). The
first LIM domain of Arrowhead (AWH): Arrowhead belongs
to the LHX protein family, which features two tandem
N-terminal LIM domains and a C-terminal DNA binding
homeodomain. Members of LHX family are found in the
nucleus and act as transcription factors or cofactors.
LHX proteins are critical for the development of
specialized cells in multiple tissue types, including
the nervous system, skeletal muscle, the heart, the
kidneys, and endocrine organs, such as the pituitary
gland and the pancreas. During embryogenesis of
Drosophila, Arrowhead is expressed in each abdominal
segment and in the labial segment. Late in embryonic
development, expression of arrowhead is refined to the
abdominal histoblasts and salivary gland imaginal ring
cells themselves. The Arrowhead gene required for
establishment of a subset of imaginal tissues: the
abdominal histoblasts and the salivary gland imaginal
rings. As in other LIM domains, this domain family is
50-60 amino acids in size and shares two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 54
Score = 62.4 bits (152), Expect = 1e-13
Identities = 25/55 (45%), Positives = 34/55 (61%), Gaps = 1/55 (1%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
C GCG I D+++L+V+ WH +CLRC C L+ +CF RD + YCK DY
Sbjct: 1 CTGCGEPITDRFLLKVS-GRSWHVSCLRCCVCQTPLERQPSCFTRDRQIYCKADY 54
Score = 24.6 bits (54), Expect = 9.7
Identities = 12/43 (27%), Positives = 21/43 (48%)
Query: 109 FVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKDDH 151
F+++ + +HV C C VC L R+ ++CK D+
Sbjct: 12 FLLKVSGRSWHVSCLRCCVCQTPLERQPSCFTRDRQIYCKADY 54
>gnl|CDD|188853 cd09469, LIM1_Lhx2, The first LIM domain of Lhx2. The first LIM
domain of Lhx2: Lhx2 belongs to the LHX protein family,
which features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as
transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
In animals, Lhx2 plays important roles in eye, cerebral
cortex, limb, the olfactory organs, and erythrocyte
development. Lhx2 gene knockout mice exhibit impaired
patterning of the cortical hem and the telencephalon of
the developing brain, and a lack of development in
olfactory structures. The Lhx2 protein has been shown
to bind to the mouse M71 olfactory receptor promoter.
Similar to other LIM domains, this domain family is
50-60 amino acids in size and share two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 64
Score = 62.3 bits (151), Expect = 1e-13
Identities = 31/59 (52%), Positives = 39/59 (66%), Gaps = 1/59 (1%)
Query: 3 RLSLCVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
R +LC GCGG+I D+Y L +A D +WH CL+C EC L+ TCF +DG YCK DY
Sbjct: 7 RAALCAGCGGKISDRYYL-LAVDKQWHMRCLKCCECKLNLESELTCFSKDGSIYCKEDY 64
>gnl|CDD|215907 pfam00412, LIM, LIM domain. This family represents two copies of
the LIM structural domain.
Length = 58
Score = 60.1 bits (146), Expect = 9e-13
Identities = 25/55 (45%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
C GCG I+D+ ++R A WH C RCA C + L F +DGK YCK DY
Sbjct: 1 CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPLGPG-DFFEKDGKLYCKHDY 54
Score = 47.3 bits (113), Expect = 5e-08
Identities = 23/56 (41%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKDDHE 152
C C + V RA K++H +CF C VCGK L PGD F ++ L+CK D+
Sbjct: 1 CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPLGPGD-FFEKDGKLYCKHDYF 55
>gnl|CDD|188763 cd09377, LIM2_Lhx2_Lhx9, The second LIM domain of Lhx2 and Lhx9
family. The second LIM domain of Lhx2 and Lhx9 family:
Lhx2 and Lhx9 are highly homologous LHX regulatory
proteins. They belong to the LHX protein family, which
features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as transcription
factors or cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs, such as
the pituitary gland and the pancreas. Although Lhx2 and
Lhx9 are highly homologous, they seems to play
regulatory roles in different organs. In animals, Lhx2
plays important roles in eye, cerebral cortex, limb, the
olfactory organs, and erythrocyte development. Lhx2 gene
knockout mice exhibit impaired patterning of the
cortical hem and the telencephalon of the developing
brain, and a lack of development in olfactory
structures. Lhx9 is expressed in several regions of the
developing mouse brain, the spinal cord, the pancreas,
in limb mesenchyme, and in the urogenital region. Lhx9
plays critical roles in gonad development. Homozygous
mice lacking functional Lhx9 alleles exhibit numerous
urogenital defects, such as gonadal agenesis,
infertility, and undetectable levels of testosterone and
estradiol coupled with high FSH levels. Lhx9 null mice
are phenotypically female, even those that are
genotypically male. As in other LIM domains, this domain
family is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein.
Length = 59
Score = 59.6 bits (145), Expect = 1e-12
Identities = 19/53 (35%), Positives = 33/53 (62%)
Query: 96 KCEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCK 148
+C +C+L + VMRA++ ++H+ CF C C K L GD F +R+ ++C+
Sbjct: 4 RCARCHLGISASELVMRARDLVFHLNCFTCATCNKPLTKGDHFGMRDGLVYCR 56
Score = 30.3 bits (69), Expect = 0.088
Identities = 18/55 (32%), Positives = 26/55 (47%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
C C I ++ A DL +H C CA C++ L + +RDG YC+ Y
Sbjct: 5 CARCHLGISASELVMRARDLVFHLNCFTCATCNKPLTKGDHFGMRDGLVYCRLHY 59
>gnl|CDD|188854 cd09470, LIM1_Lhx9, The first LIM domain of Lhx9. The first LIM
domain of Lhx9: Lhx9 belongs to the LHX protein family,
which features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as
transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
Lhx9 is highly homologous to Lhx2. It is expressed in
several regions of the developing mouse brain, the
spinal cord, the pancreas, in limb mesenchyme, and in
the urogenital region. Lhx9 plays critical roles in
gonad development. Homozygous mice lacking functional
Lhx9 alleles exhibit numerous urogenital defects, such
as gonadal agenesis, infertility, and undetectable
levels of testosterone and estradiol coupled with high
FSH levels. Lhx9 null mice have reduced levels of the
Sf1 nuclear receptor that is required for
gonadogenesis, and recent studies have shown that Lhx9
is able to activate the Sf1/FtzF1 gene. Lhx9 null mice
are phenotypically female, even those that are
genotypically male. As in other LIM domains, this
domain family is 50-60 amino acids in size and shares
two characteristic zinc finger motifs. The two zinc
fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to
two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric
protein.
Length = 54
Score = 57.0 bits (137), Expect = 1e-11
Identities = 29/55 (52%), Positives = 36/55 (65%), Gaps = 1/55 (1%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
C GCGG+I D+Y L +A D +WH CL+C EC L+ TCF +DG YCK DY
Sbjct: 1 CAGCGGKISDRYYL-LAVDKQWHLRCLKCCECKLALESELTCFAKDGSIYCKEDY 54
>gnl|CDD|188764 cd09378, LIM2_Lmx1a_Lmx1b, The second LIM domain of Lmx1a and
Lmx1b. The second LIM domain of Lmx1a and Lmx1b: Lmx1a
and Lmx1b belong to the LHX protein family, which
features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as transcription
factors or cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs such as the
pituitary gland and the pancreas. Mouse Lmx1a is
expressed in multiple tissues, including the roof plate
of the neural tube, the developing brain, the otic
vesicles, the notochord, and the pancreas. In mouse,
mutations in Lmx1a result in failure of the roof plate
to develop. Lmx1a may act upstream of other roof plate
markers such as MafB, Gdf7, Bmp6, and Bmp7. Further
characterization of these mice reveals numerous defects
including disorganized cerebellum, hippocampus, and
cortex; altered pigmentation; female sterility, skeletal
defects, and behavioral abnormalities. In the mouse,
Lmx1b functions in the developing limbs and eyes, the
kidneys, the brain, and in cranial mesenchyme. The
disruption of Lmx1b gene results kidney and limb
defects. In the brain, Lmx1b is important for generation
of mesencephalic dopamine neurons and the
differentiation of serotonergic neurons. In the mouse
eye, Lmx1b regulates anterior segment (cornea, iris,
ciliary body, trabecular meshwork, and lens)
development. As in other LIM domains, this domain family
is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein.
Length = 55
Score = 56.7 bits (137), Expect = 2e-11
Identities = 26/55 (47%), Positives = 33/55 (60%)
Query: 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKDDH 151
C C + VMRA +YH++CFCC VC +QL GDEF L+E L CK D+
Sbjct: 1 CSGCLEKIAPSELVMRALENVYHLRCFCCCVCERQLQKGDEFVLKEGQLLCKSDY 55
Score = 27.0 bits (60), Expect = 1.4
Identities = 15/55 (27%), Positives = 26/55 (47%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
C GC +I ++ A + +H C C C + L + +++G+ CK DY
Sbjct: 1 CSGCLEKIAPSELVMRALENVYHLRCFCCCVCERQLQKGDEFVLKEGQLLCKSDY 55
>gnl|CDD|188773 cd09387, LIM2_LMO4, The second LIM domain of LMO4 (LIM domain only
protein 4). The second LIM domain of LMO4 (LIM domain
only protein 4): LMO4 is a nuclear protein that plays
important roles in transcriptional regulation and
development. LMO4 is involved in various functions in
tumorigenesis and cellular differentiation. LMO4
proteins regulate gene expression by interacting with a
wide variety of transcription factors and cofactors to
form large transcription complexes. It can interact with
Smad proteins, and associate with the promoter of the
PAI-1 (plasminogen activator inhibitor-1) gene in a
TGFbeta (transforming growth factor beta)-dependent
manner. LMO4 can also form a complex with transcription
regulator CREB (cAMP response element-binding protein)
and interact with CLIM1 and CLIM2. In breast tissue,
LMO4 interacts with multiple proteins, including the
cofactor CtIP [CtBP (C-terminal binding
protein)-interacting protein], the breast and ovarian
tumor suppressor BRCA1 (breast-cancer susceptibility
gene 1) and the LIM-domain-binding protein LDB1.
Functionally, LMO4 is shown to repress BRCA1-mediated
transcription activation, thus invoking a potential role
for LMO4 as a negative regulator of BRCA1 in sporadic
breast cancer. LMO4 also forms complex to both ERa
(oestrogen receptor alpha), MTA1 (metastasis tumor
antigen 1), and HDACs (histone deacetylases), implying
that LMO4 is also a component of the MTA1 corepressor
complex. Over-expressed LMO4 represses ERa
transactivation functions in an HDAC-dependent manner,
and contributes to the process of breast cancer
progression by allowing the development of Era-negative
phenotypes. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 55
Score = 55.6 bits (134), Expect = 4e-11
Identities = 23/55 (41%), Positives = 30/55 (54%)
Query: 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKDDH 151
C C + + VMRA+ +YH++CF C C QLVPGD F LFC+ D
Sbjct: 1 CSACGQSIPASELVMRAQGNVYHLKCFTCSTCHNQLVPGDRFHYVNGSLFCEHDR 55
Score = 25.5 bits (56), Expect = 4.8
Identities = 14/55 (25%), Positives = 24/55 (43%), Gaps = 2/55 (3%)
Query: 7 CVGCGGQI-HDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRD 60
C CG I + ++R ++ +H C C+ CH L +G +C+ D
Sbjct: 1 CSACGQSIPASELVMRAQGNV-YHLKCFTCSTCHNQLVPGDRFHYVNGSLFCEHD 54
>gnl|CDD|188765 cd09379, LIM2_AWH, The second LIM domain of Arrowhead (AWH). The
second LIM domain of Arrowhead (AWH): Arrowhead belongs
to the LHX protein family, which features two tandem
N-terminal LIM domains and a C-terminal DNA binding
homeodomain. Members of LHX family are found in the
nucleus and act as transcription factors or cofactors.
LHX proteins are critical for the development of
specialized cells in multiple tissue types, including
the nervous system, skeletal muscle, the heart, the
kidneys, and endocrine organs such as the pituitary
gland and the pancreas. During embryogenesis of
Drosophila, Arrowhead is expressed in each abdominal
segment and in the labial segment. Late in embryonic
development, expression of arrowhead is refined to the
abdominal histoblasts and salivary gland imaginal ring
cells themselves. The Arrowhead gene required for
establishment of a subset of imaginal tissues: the
abdominal histoblasts and the salivary gland imaginal
rings. As in other LIM domains, this domain family is
50-60 amino acids in size and shares two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 55
Score = 55.1 bits (133), Expect = 7e-11
Identities = 25/52 (48%), Positives = 34/52 (65%)
Query: 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCK 148
C KC+ N D+V RA++ +YH+ CF C C +QL G+EFAL ED + CK
Sbjct: 1 CAKCSRNISASDWVRRARDHVYHLACFACDACKRQLSTGEEFALIEDRVLCK 52
Score = 27.4 bits (61), Expect = 0.90
Identities = 15/55 (27%), Positives = 21/55 (38%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
C C I +R A D +H AC C C + L + + + CK Y
Sbjct: 1 CAKCSRNISASDWVRRARDHVYHLACFACDACKRQLSTGEEFALIEDRVLCKAHY 55
>gnl|CDD|188762 cd09376, LIM2_Lhx3_Lhx4, The second LIM domain of Lhx3-Lhx4 family.
The second LIM domain of Lhx3-Lhx4 family: Lhx3 and
Lhx4 belong to the LHX protein family, which features
two tandem N-terminal LIM domains and a C-terminal DNA
binding homeodomain. Members of LHX family are found in
the nucleus and act as transcription factors or
cofactors. LHX proteins are critical for the development
of specialized cells in multiple tissue types, including
the nervous system, skeletal muscle, the heart, the
kidneys, and endocrine organs, such as the pituitary
gland and the pancreas. The LHX3 and LHX4
LIM-homeodomain transcription factors play essential
roles in pituitary gland and nervous system development.
Although LHX3 and LHX4 share marked sequence homology,
the genes have different expression patterns. They play
overlapping, but distinct functions during the
establishment of the specialized cells of the mammalian
pituitary gland and the nervous system. Lhx3 proteins
have been demonstrated the ability to directly bind to
the promoters/enhancers of several pituitary hormone
gene promoters to cause increased transcription.Lhx3a
and Lhx3b, whose mRNAs have distinct temporal expression
profiles during development, are two isoforms of Lhx3.
LHX4 plays essential roles in pituitary gland and
nervous system development. In mice, the lhx4 gene is
expressed in the developing hindbrain, cerebral cortex,
pituitary gland, and spinal cord. LHX4 shows significant
sequence similarity to LHX3, particularly to isoforms
Lhx3a. In gene regulation experiments, the LHX4 protein
exhibits regulation roles towards pituitary genes,
acting on their promoters/enhancers. As in other LIM
domains, this domain family is 50-60 amino acids in size
and shares two characteristic zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 56
Score = 54.7 bits (132), Expect = 8e-11
Identities = 24/56 (42%), Positives = 33/56 (58%), Gaps = 1/56 (1%)
Query: 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDG-LFCKDDH 151
C C+ V RA++ +YH++CF C +C +QL GDEF L ED L CK D+
Sbjct: 1 CAGCDEGIPPTQVVRRAQDNVYHLECFACFMCKRQLETGDEFYLMEDDRLVCKKDY 56
Score = 29.6 bits (67), Expect = 0.14
Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 1/56 (1%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCF-VRDGKTYCKRDY 61
C GC I ++R A D +H C C C + L+ + + D + CK+DY
Sbjct: 1 CAGCDEGIPPTQVVRRAQDNVYHLECFACFMCKRQLETGDEFYLMEDDRLVCKKDY 56
>gnl|CDD|188761 cd09375, LIM2_Lhx1_Lhx5, The second LIM domain of Lhx1 (also known
as Lim1) and Lhx5. The second LIM domain of Lhx1 (also
known as Lim1) and Lhx5. Lhx1 and Lhx5 are closely
related members of LHX protein family, which features
two tandem N-terminal LIM domains and a C-terminal DNA
binding homeodomain. Members of LHX family are found in
the nucleus and act as transcription factors or
cofactors. LHX proteins are critical for the development
of specialized cells in multiple tissue types, including
the nervous system, skeletal muscle, the heart, the
kidneys, and endocrine organs, such as the pituitary
gland and the pancreas. Lhx1 is required for regulating
the vertebrate head organizer, the nervous system, and
female reproductive tract development. During
embryogenesis in the mouse, Lhx1 is expressed early in
mesodermal tissue, then later during urogenital, kidney,
liver, and nervous system development. In the adult,
expression is restricted to the kidney and brain. A
mouse embryos with Lhx1 gene knockout cannot grow normal
anterior head structures, kidneys, and gonads, but with
normally developed trunk and tail morphology. In the
developing nervous system, Lhx1 is required to direct
the trajectories of motor axons in the limb. Lhx1 null
female mice lack the oviducts and uterus. Lhx5 protein
may play complementary or overlapping roles with Lhx1.
The expression of Lhx5 in the anterior portion of the
mouse neural tube suggests a role in patterning of the
forebrain. All LIM domains are 50-60 amino acids in size
and share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 56
Score = 54.3 bits (131), Expect = 1e-10
Identities = 22/56 (39%), Positives = 35/56 (62%), Gaps = 1/56 (1%)
Query: 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLF-CKDDH 151
C C+ D V RA++K++H+ CF C+VC KQL G+E + ++ F CK+D+
Sbjct: 1 CAGCDQGISPNDLVRRARDKVFHLNCFTCMVCRKQLSTGEELYILDENKFICKEDY 56
Score = 28.5 bits (64), Expect = 0.37
Identities = 17/56 (30%), Positives = 24/56 (42%), Gaps = 1/56 (1%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTY-CKRDY 61
C GC I ++R A D +H C C C + L ++ D + CK DY
Sbjct: 1 CAGCDQGISPNDLVRRARDKVFHLNCFTCMVCRKQLSTGEELYILDENKFICKEDY 56
>gnl|CDD|188757 cd09371, LIM1_Lmx1b, The first LIM domain of Lmx1b. The first
LIM domain of Lmx1b: Lmx1b belongs to the LHX protein
family, which features two tandem N-terminal LIM
domains and a C-terminal DNA binding homeodomain.
Members of LHX family are found in the nucleus and act
as transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
In mouse, Lmx1b functions in the developing limbs and
eyes, the kidneys, the brain, and in cranial
mesenchyme. The disruption of Lmx1b gene results kidney
and limb defects. In the brain, Lmx1b is important for
generation of mesencephalic dopamine neurons and the
differentiation of serotonergic neurons. In the mouse
eye, Lmx1b regulates anterior segment (cornea, iris,
ciliary body, trabecular meshwork, and lens)
development. As in other LIM domains, this domain
family is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein.
Length = 53
Score = 53.9 bits (130), Expect = 2e-10
Identities = 26/55 (47%), Positives = 34/55 (61%), Gaps = 3/55 (5%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
C GC I D+Y+LRV + WH CL+C+ C Q L +C+ RD K YCK+DY
Sbjct: 1 CAGCQRPISDRYLLRVN-ERSWHEECLQCSVCQQPLTT--SCYFRDRKLYCKQDY 52
>gnl|CDD|188856 cd09472, LIM2_Lhx3b, The second LIM domain of Lhx3b. The second
LIM domain of Lhx3b. Lhx3b is a member of LHX protein
family, which features two tandem N-terminal LIM domains
and a C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as transcription
factors or cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs, such as
the pituitary gland and the pancreas. Lhx3b is one of
the two isoforms of Lhx3. The Lhx3 gene is expressed in
the ventral spinal cord, the pons, the medulla
oblongata, and the pineal gland of the developing
nervous system during mouse embryogenesis, and
transcripts are found in the emergent pituitary gland.
Lhx3 functions in concert with other transcription
factors to specify interneuron and motor neuron fates
during development. Lhx3 proteins have been demonstrated
to directly bind to the promoters of several pituitary
hormone gene promoters. The Lhx3 gene encodes two
isoforms, LHX3a and LHX3b that differ in their
amino-terminal sequences, where Lhx3a has longer
N-terminal. They show differential activation of
pituitary hormone genes and distinct DNA binding
properties. In human, Lhx3a trans-activated the
alpha-glycoprotein subunit promoter and genes containing
a high-affinity Lhx3 binding site more effectively than
the hLhx3b isoform. In addition, hLhx3a induce
transcription of the TSHbeta-subunit gene by acting on
pituitary POU domain factor, Pit-1, while hLhx3b does
not. As in other LIM domains, this domain family is
50-60 amino acids in size and shares two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 57
Score = 53.5 bits (128), Expect = 2e-10
Identities = 26/57 (45%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 96 KCEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDG-LFCKDDH 151
KC C V RA++ +YH+ CF C+VC +QL GDEF L ED L CK D+
Sbjct: 1 KCAACQQGIPPTQVVRRAQDFVYHLHCFACIVCKRQLATGDEFYLMEDSRLVCKADY 57
>gnl|CDD|188859 cd09475, LIM2_Lhx9, The second LIM domain of Lhx9. The second LIM
domain of Lhx9: Lhx9 belongs to the LHX protein family,
which features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as transcription
factors or cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs, such as
the pituitary gland and the pancreas. Lhx9 is highly
homologous to Lhx2. It is expressed in several regions
of the developing mouse brain, the spinal cord, the
pancreas, in limb mesenchyme, and in the urogenital
region. Lhx9 plays critical roles in gonad development.
Homozygous mice lacking functional Lhx9 alleles exhibit
numerous urogenital defects, such as gonadal agenesis,
infertility, and undetectable levels of testosterone and
estradiol coupled with high FSH levels. Lhx9 null mice
have reduced levels of the Sf1 nuclear receptor that is
required for gonadogenesis, and recent studies have
shown that Lhx9 is able to activate the Sf1/FtzF1 gene.
Lhx9 null mice are phenotypically female, even those
that are genotypically male. As in other LIM domains,
this domain family is 50-60 amino acids in size and
shares two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 59
Score = 52.4 bits (125), Expect = 7e-10
Identities = 19/53 (35%), Positives = 33/53 (62%)
Query: 96 KCEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCK 148
+C +C+L + VMRA+ +YH+ CF C C K L GD F ++++ ++C+
Sbjct: 4 RCARCHLGISASEMVMRARESVYHLSCFTCTTCNKTLTTGDHFGMKDNLVYCR 56
>gnl|CDD|188756 cd09370, LIM1_Lmx1a, The first LIM domain of Lmx1a. The first
LIM domain of Lmx1a: Lmx1a belongs to the LHX protein
family, which features two tandem N-terminal LIM
domains and a C-terminal DNA binding homeodomain.
Members of LHX family are found in the nucleus and act
as transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
Mouse Lmx1a is expressed in multiple tissues, including
the roof plate of the neural tube, the developing
brain, the otic vesicles, the notochord, and the
pancreas. Human Lmx1a can be found in pancreas,
skeletal muscle, adipose tissue, developing brain,
mammary glands, and pituitary. The functions of Lmx1a
in the developing nervous system were revealed by
studies of mutant mouse. In mouse, mutations in Lmx1a
result in failure of the roof plate to develop. Lmx1a
may act upstream of other roof plate markers such as
MafB, Gdf7, Bmp 6, and Bmp7. Further characterization
of these mice reveals numerous defects including
disorganized cerebellum, hippocampus, and cortex;
altered pigmentation; female sterility; skeletal
defects; and behavioral abnormalities. Within
pancreatic cells, the Lmx1a protein interacts
synergistically with the bHLH transcription factor E47
to activate the insulin gene enhancer/promoter. As in
other LIM domains, this domain family is 50-60 amino
acids in size and shares two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 52
Score = 50.9 bits (122), Expect = 2e-09
Identities = 28/55 (50%), Positives = 34/55 (61%), Gaps = 3/55 (5%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
C GC I D+++LRV L WH CL+CA C + L+ TCF RD K YCK DY
Sbjct: 1 CEGCNRVIQDRFLLRVNDSL-WHERCLQCASCKEPLET--TCFYRDKKLYCKEDY 52
>gnl|CDD|188857 cd09473, LIM2_Lhx4, The second LIM domain of Lhx4. The second LIM
domain of Lhx4. Lhx4 belongs to the LHX protein family,
which features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as transcription
factors or cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs, such as
the pituitary gland and the pancreas. LHX4 plays
essential roles in pituitary gland and nervous system
development. In mice, the lhx4 gene is expressed in the
developing hindbrain, cerebral cortex, pituitary gland,
and spinal cord. LHX4 shows significant sequence
similarity to LHX3, particularly to isoforms Lhx3a. In
gene regulation experiments, the LHX4 protein exhibits
regulation roles towards pituitary genes, acting on
their promoters/enhancers. As in other LIM domains, this
domain family is 50-60 amino acids in size and shares
two characteristic zinc finger motifs. The two zinc
fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 56
Score = 51.2 bits (122), Expect = 2e-09
Identities = 24/56 (42%), Positives = 34/56 (60%), Gaps = 1/56 (1%)
Query: 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDG-LFCKDDH 151
C C V +A++ +YH+ CF C++C +QL GDEF L EDG L CK+D+
Sbjct: 1 CTACQQGIPPTQVVRKAQDFVYHLHCFACIICSRQLATGDEFYLMEDGRLVCKEDY 56
Score = 28.8 bits (64), Expect = 0.28
Identities = 17/56 (30%), Positives = 24/56 (42%), Gaps = 1/56 (1%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFV-RDGKTYCKRDY 61
C C I ++R A D +H C C C + L ++ DG+ CK DY
Sbjct: 1 CTACQQGIPPTQVVRKAQDFVYHLHCFACIICSRQLATGDEFYLMEDGRLVCKEDY 56
>gnl|CDD|214528 smart00132, LIM, Zinc-binding domain present in Lin-11, Isl-1,
Mec-3. Zinc-binding domain family. Some LIM domains
bind protein partners via tyrosine-containing motifs.
LIM domains are found in many key regulators of
developmental pathways.
Length = 54
Score = 50.5 bits (121), Expect = 4e-09
Identities = 22/55 (40%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 96 KCEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKDD 150
KC C + V+RA K++H +CF C CGK L GD F ++ L+CKD
Sbjct: 1 KCAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLS-GDTFFEKDGKLYCKDC 54
Score = 48.9 bits (117), Expect = 1e-08
Identities = 21/54 (38%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRD 60
C GCG I+ + A WH C +CA C + L + T F +DGK YCK
Sbjct: 2 CAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLSGD-TFFEKDGKLYCKDC 54
Score = 24.7 bits (54), Expect = 8.4
Identities = 14/55 (25%), Positives = 23/55 (41%), Gaps = 1/55 (1%)
Query: 34 RCAECHQFLDENCTCFVRDGKTYCKRDYVSSEKNQFLDENCTCFVRDGKTYCKRD 88
+CA C + + GK + + + + L + T F +DGK YCK
Sbjct: 1 KCAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLSGD-TFFEKDGKLYCKDC 54
>gnl|CDD|188858 cd09474, LIM2_Lhx2, The second LIM domain of Lhx2. The second LIM
domain of Lhx2: Lhx2 belongs to the LHX protein family,
which features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as transcription
factors or cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs, such as
the pituitary gland and the pancreas. In animals, Lhx2
plays important roles in eye, cerebral cortex, limb, the
olfactory organs, and erythrocyte development. Lhx2 gene
knockout mice exhibit impaired patterning of the
cortical hem and the telencephalon of the developing
brain, and a lack of development in olfactory
structures. The Lhx2 protein has been shown to bind to
the mouse M71 olfactory receptor promoter. Similar to
other LIM domains, this domain family is 50-60 amino
acids in size and shares two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 59
Score = 50.5 bits (120), Expect = 4e-09
Identities = 19/53 (35%), Positives = 34/53 (64%)
Query: 96 KCEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCK 148
+C +C+L + VMRA++ +YH+ CF C C K L GD F ++++ ++C+
Sbjct: 4 RCARCHLGISASEMVMRARDLVYHLNCFTCTTCNKMLTTGDHFGMKDNLVYCR 56
Score = 25.4 bits (55), Expect = 5.7
Identities = 14/52 (26%), Positives = 22/52 (42%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCK 58
C C I ++ A DL +H C C C++ L ++D YC+
Sbjct: 5 CARCHLGISASEMVMRARDLVYHLNCFTCTTCNKMLTTGDHFGMKDNLVYCR 56
>gnl|CDD|188850 cd09466, LIM1_Lhx3a, The first LIM domain of Lhx3a. The first
LIM domain of Lhx3a: Lhx3a is a member of LHX protein
family, which features two tandem N-terminal LIM
domains and a C-terminal DNA binding homeodomain.
Members of LHX family are found in the nucleus and act
as transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
Lhx3a is one of the two isoforms of Lhx3. The Lhx3 gene
is expressed in the ventral spinal cord, the pons, the
medulla oblongata, and the pineal gland of the
developing nervous system during mouse embryogenesis,
and transcripts are found in the emergent pituitary
gland. Lhx3 functions in concert with other
transcription factors to specify interneuron and motor
neuron fates during development. Lhx3 proteins have
been demonstrated to directly bind to the promoters of
several pituitary hormone gene promoters. The Lhx3 gene
encodes two isoforms, LHX3a and LHX3b that differ in
their amino-terminal sequences, where Lhx3a has longer
N-terminal. They show differential activation of
pituitary hormone genes and distinct DNA binding
properties. In human, Lhx3a trans-activated the
alpha-glycoprotein subunit promoter and genes
containing a high-affinity Lhx3 binding site more
effectively than the hLhx3b isoform. In addition,
hLhx3a induce transcription of the TSHbeta-subunit gene
by acting on pituitary POU domain factor, Pit-1, while
hLhx3b does not. As in other LIM domains, this domain
family is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein.
Length = 56
Score = 50.2 bits (120), Expect = 5e-09
Identities = 24/58 (41%), Positives = 34/58 (58%), Gaps = 3/58 (5%)
Query: 4 LSLCVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
+ C GC I D++IL+V D WH+ CL+C +C L + CF R G+ YCK D+
Sbjct: 1 IPKCAGCDHPIFDRFILKVQ-DKPWHSKCLKCVDCQAQLTDK--CFSRGGQVYCKEDF 55
Score = 30.9 bits (70), Expect = 0.052
Identities = 14/42 (33%), Positives = 25/42 (59%), Gaps = 2/42 (4%)
Query: 109 FVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKDD 150
F+++ ++K +H +C CV C QL D+ R ++CK+D
Sbjct: 15 FILKVQDKPWHSKCLKCVDCQAQLT--DKCFSRGGQVYCKED 54
>gnl|CDD|188852 cd09468, LIM1_Lhx4, The first LIM domain of Lhx4. The first LIM
domain of Lhx4. Lhx4 belongs to the LHX protein family,
which features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as
transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
LHX4 plays essential roles in pituitary gland and
nervous system development. In mice, the lhx4 gene is
expressed in the developing hindbrain, cerebral cortex,
pituitary gland, and spinal cord. LHX4 shows
significant sequence similarity to LHX3, particularly
to isoforms Lhx3a. In gene regulation experiments, the
LHX4 protein exhibits regulation roles towards
pituitary genes, acting on their promoters/enhancers.
As in other LIM domains, this domain family is 50-60
amino acids in size and shares two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 52
Score = 50.0 bits (119), Expect = 6e-09
Identities = 26/55 (47%), Positives = 34/55 (61%), Gaps = 3/55 (5%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
C GC I D++IL+V D WH++CL+CA+C L E CF R G YCK D+
Sbjct: 1 CAGCNQHILDKFILKVL-DRHWHSSCLKCADCQMQLAER--CFSRAGNVYCKEDF 52
>gnl|CDD|188711 cd08368, LIM, LIM is a small protein-protein interaction domain,
containing two zinc fingers. LIM domains are
identified in a diverse group of proteins with wide
variety of biological functions, including gene
expression regulation, cell fate determination,
cytoskeleton organization, tumor formation and
development. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes. They perform their functions through
interactions with other protein partners. LIM domains
are 50-60 amino acids in size and share two
characteristic highly conserved zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. The consensus sequence of LIM
domain has been defined as
C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,
21)-C-x(2,3)-[CHD] (where X denotes any amino acid).
Length = 53
Score = 49.2 bits (118), Expect = 8e-09
Identities = 20/55 (36%), Positives = 32/55 (58%), Gaps = 2/55 (3%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
C GCG I + +LR A +WH C +C+ C + L + + + +DGK YC++ Y
Sbjct: 1 CAGCGKPIEGRELLR-ALGKKWHPECFKCSVCGKPLGGD-SFYEKDGKPYCEKCY 53
Score = 46.9 bits (112), Expect = 6e-08
Identities = 18/55 (32%), Positives = 27/55 (49%), Gaps = 2/55 (3%)
Query: 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKDDH 151
C C ++RA K +H +CF C VCGK L GD F ++ +C+ +
Sbjct: 1 CAGCGKPI-EGRELLRALGKKWHPECFKCSVCGKPLG-GDSFYEKDGKPYCEKCY 53
>gnl|CDD|188754 cd09368, LIM1_Lhx3_Lhx4, The first LIM domain of Lhx3 and Lhx4
family. The first LIM domain of Lhx3-Lhx4 family: Lhx3
and Lhx4 belong to the LHX protein family, which
features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as
transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
The LHX3 and LHX4 LIM-homeodomain transcription factors
play essential roles in pituitary gland and nervous
system development. Although LHX3 and LHX4 share marked
sequence homology, the genes have different expression
patterns. They play overlapping, but distinct functions
during the establishment of the specialized cells of
the mammalian pituitary gland and the nervous system.
Lhx3 proteins have been demonstrated the ability to
directly bind to the promoters/enhancers of several
pituitary hormone gene promoters to cause increased
transcription. Lhx3a and Lhx3b, whose mRNAs have
distinct temporal expression profiles during
development, are two isoforms of Lhx3. LHX4 plays
essential roles in pituitary gland and nervous system
development. In mice, the lhx4 gene is expressed in the
developing hindbrain, cerebral cortex, pituitary gland,
and spinal cord. LHX4 shows significant sequence
similarity to LHX3, particularly to isoforms Lhx3a. In
gene regulation experiments, the LHX4 protein exhibits
regulation roles towards pituitary genes, acting on
their promoters/enhancers. As in other LIM domains,
this domain family is 50-60 amino acids in size and
shares two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to
two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric
protein.
Length = 52
Score = 49.0 bits (117), Expect = 1e-08
Identities = 25/55 (45%), Positives = 33/55 (60%), Gaps = 3/55 (5%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
C GC I D++IL+V D WHA CL+C +C L + CF R+G YCK D+
Sbjct: 1 CGGCQEHILDRFILKVL-DRTWHAKCLKCNDCGAQLTDK--CFARNGHVYCKDDF 52
Score = 26.6 bits (59), Expect = 1.5
Identities = 14/42 (33%), Positives = 24/42 (57%), Gaps = 2/42 (4%)
Query: 109 FVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKDD 150
F+++ ++ +H +C C CG QL D+ R ++CKDD
Sbjct: 12 FILKVLDRTWHAKCLKCNDCGAQLT--DKCFARNGHVYCKDD 51
>gnl|CDD|188769 cd09383, LIM2_Lhx7_Lhx8, The second LIM domain of Lhx7 and Lhx8.
The second LIM domain of Lhx7 and Lhx8: Lhx7 and Lhx8
belong to the LHX protein family, which features two
tandem N-terminal LIM domains and a C-terminal DNA
binding homeodomain. Members of LHX family are found in
the nucleus and act as transcription factors or
cofactors. LHX proteins are critical for the development
of specialized cells in multiple tissue types, including
the nervous system, skeletal muscle, the heart, the
kidneys, and endocrine organs such as the pituitary
gland and the pancreas. Studies using mutant mice have
revealed roles for Lhx7 and Lhx8 in the development of
cholinergic neurons in the telencephalon and in basal
forebrain development. Mice lacking alleles of the
LIM-homeobox gene Lhx7 or Lhx8 display dramatically
reduced number of forebrain cholinergic neurons. In
addition, Lhx7 mutation affects male and female mice
differently, with females appearing more affected than
males. As in other LIM domains, this domain family is
50-60 amino acids in size and shares two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 55
Score = 48.9 bits (116), Expect = 1e-08
Identities = 22/52 (42%), Positives = 32/52 (61%)
Query: 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCK 148
C +C + D+V RAK +YH+ CF C C +QL G+EFAL E+ + C+
Sbjct: 1 CSRCGRHIHSTDWVRRAKGNVYHLACFACFSCKRQLSTGEEFALVEEKVLCR 52
Score = 25.8 bits (56), Expect = 3.8
Identities = 16/55 (29%), Positives = 22/55 (40%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
C CG IH +R A +H AC C C + L + + K C+ Y
Sbjct: 1 CSRCGRHIHSTDWVRRAKGNVYHLACFACFSCKRQLSTGEEFALVEEKVLCRVHY 55
>gnl|CDD|188767 cd09381, LIM1_Lhx7_Lhx8, The first LIM domain of Lhx7 and Lhx8.
The first LIM domain of Lhx7 and Lhx8: Lhx7 and Lhx8
belong to the LHX protein family, which features two
tandem N-terminal LIM domains and a C-terminal DNA
binding homeodomain. Members of LHX family are found in
the nucleus and act as transcription factors or
cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs such as
the pituitary gland and the pancreas. Studies using
mutant mice have revealed roles for Lhx7 and Lhx8 in
the development of cholinergic neurons in the
telencephalon and in basal forebrain development. Mice
lacking alleles of the LIM-homeobox gene Lhx7 or Lhx8
display dramatically reduced number of forebrain
cholinergic neurons. In addition, Lhx7 mutation affects
male and female mice differently, with females
appearing more affected than males. As in other LIM
domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein.
Length = 56
Score = 48.4 bits (115), Expect = 2e-08
Identities = 23/56 (41%), Positives = 35/56 (62%), Gaps = 1/56 (1%)
Query: 6 LCVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
+C CG +I D+Y+L+V DL WH CL C+ C L + +C+++D +CK DY
Sbjct: 1 VCSSCGLEIVDKYLLKVN-DLCWHVRCLSCSVCRTSLGRHTSCYIKDKDIFCKLDY 55
Score = 25.3 bits (55), Expect = 6.1
Identities = 11/45 (24%), Positives = 24/45 (53%)
Query: 107 EDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKDDH 151
+ ++++ + +HV+C C VC L +++ +FCK D+
Sbjct: 11 DKYLLKVNDLCWHVRCLSCSVCRTSLGRHTSCYIKDKDIFCKLDY 55
>gnl|CDD|188753 cd09367, LIM1_Lhx1_Lhx5, The first LIM domain of Lhx1 (also known
as Lim1) and Lhx5. The first LIM domain of Lhx1 (also
known as Lim1) and Lhx5. Lhx1 and Lhx5 are closely
related members of LHX protein family, which features
two tandem N-terminal LIM domains and a C-terminal DNA
binding homeodomain. Members of LHX family are found in
the nucleus and act as transcription factors or
cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs, such as
the pituitary gland and the pancreas. Lhx1 is required
for regulating the vertebrate head organizer, the
nervous system, and female reproductive tract
development. During embryogenesis in the mouse, Lhx1 is
expressed early in mesodermal tissue, then later during
urogenital, kidney, liver, and nervous system
development. In the adult, expression is restricted to
the kidney and brain. A mouse embryos with Lhx1 gene
knockout cannot grow normal anterior head structures,
kidneys, and gonads, but with normally developed trunk
and tail morphology. In the developing nervous system,
Lhx1 is required to direct the trajectories of motor
axons in the limb. Lhx1 null female mice lack the
oviducts and uterus. Lhx5 protein may play
complementary or overlapping roles with Lhx1. The
expression of Lhx5 in the anterior portion of the mouse
neural tube suggests a role in patterning of the
forebrain. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 52
Score = 47.8 bits (114), Expect = 3e-08
Identities = 24/55 (43%), Positives = 33/55 (60%), Gaps = 3/55 (5%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
C GC I D+++L V D WHA C++C +C L E CF R+GK YC+ D+
Sbjct: 1 CAGCDRPILDKFLLNVL-DRAWHAKCVQCCDCKCPLTEK--CFSREGKLYCRNDF 52
>gnl|CDD|188772 cd09386, LIM1_LMO4, The first LIM domain of LMO4 (LIM domain only
protein 4). The first LIM domain of LMO4 (LIM domain
only protein 4): LMO4 is a nuclear protein that plays
important roles in transcriptional regulation and
development. LMO4 is involved in various functions in
tumorigenesis and cellular differentiation. LMO4
proteins regulate gene expression by interacting with a
wide variety of transcription factors and cofactors to
form large transcription complexes. It can interact
with Smad proteins, and associate with the promoter of
the PAI-1 (plasminogen activator inhibitor-1) gene in a
TGFbeta (transforming growth factor beta)-dependent
manner. LMO4 can also form a complex with transcription
regulator CREB (cAMP response element-binding protein)
and interact with CLIM1 and CLIM2. In breast tissue,
LMO4 interacts with multiple proteins, including the
cofactor CtIP [CtBP (C-terminal binding
protein)-interacting protein], the breast and ovarian
tumor suppressor BRCA1 (breast-cancer susceptibility
gene 1) and the LIM-domain-binding protein LDB1.
Functionally, LMO4 is shown to repress BRCA1-mediated
transcription activation, thus invoking a potential
role for LMO4 as a negative regulator of BRCA1 in
sporadic breast cancer. LMO4 also forms complex to
both ERa (oestrogen receptor alpha), MTA1 (metastasis
tumor antigen 1), and HDACs (histone deacetylases),
implying that LMO4 is also a component of the MTA1
corepressor complex. Over-expressed LMO4 represses ERa
transactivation functions in an HDAC-dependent manner,
and contributes to the process of breast cancer
progression by allowing the development of Era-negative
phenotypes. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 55
Score = 46.3 bits (110), Expect = 1e-07
Identities = 24/56 (42%), Positives = 33/56 (58%), Gaps = 2/56 (3%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDE-NCTCFVRDGKTYCKRDY 61
C GCGG+I D+++L A D WH CL+C+ C L E +C+ + G CK DY
Sbjct: 1 CAGCGGKIVDRFLL-HALDRYWHNGCLKCSCCQAQLGEIGSSCYTKGGMILCKNDY 55
>gnl|CDD|188851 cd09467, LIM1_Lhx3b, The first LIM domain of Lhx3b. The first
LIM domain of Lhx3b. Lhx3b is a member of LHX protein
family, which features two tandem N-terminal LIM
domains and a C-terminal DNA binding homeodomain.
Members of LHX family are found in the nucleus and act
as transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
Lhx3b is one of the two isoforms of Lhx3. The Lhx3 gene
is expressed in the ventral spinal cord, the pons, the
medulla oblongata, and the pineal gland of the
developing nervous system during mouse embryogenesis,
and transcripts are found in the emergent pituitary
gland. Lhx3 functions in concert with other
transcription factors to specify interneuron and motor
neuron fates during development. Lhx3 proteins have
been demonstrated to directly bind to the promoters of
several pituitary hormone gene promoters. The Lhx3 gene
encodes two isoforms, LHX3a and LHX3b that differ in
their amino-terminal sequences, where Lhx3a has longer
N-terminal. They show differential activation of
pituitary hormone genes and distinct DNA binding
properties. In human, Lhx3a trans-activated the
alpha-glycoprotein subunit promoter and genes
containing a high-affinity Lhx3 binding site more
effectively than the hLhx3b isoform. In addition,
hLhx3a induce transcription of the TSHbeta-subunit gene
by acting on pituitary POU domain factor, Pit-1, while
hLhx3b does not. As in other LIM domains, this domain
family is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein.
Length = 55
Score = 45.7 bits (108), Expect = 2e-07
Identities = 25/58 (43%), Positives = 34/58 (58%), Gaps = 3/58 (5%)
Query: 4 LSLCVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
+ LC GC I D++IL+V D WH+ CL+C++C L E CF R YCK D+
Sbjct: 1 IPLCAGCNQHIVDRFILKVL-DRHWHSKCLKCSDCQTQLAEK--CFSRGDSVYCKDDF 55
Score = 26.4 bits (58), Expect = 2.2
Identities = 16/54 (29%), Positives = 29/54 (53%), Gaps = 3/54 (5%)
Query: 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKDD 150
C CN + + F+++ ++ +H +C C C QL ++ R D ++CKDD
Sbjct: 4 CAGCNQHIV-DRFILKVLDRHWHSKCLKCSDCQTQL--AEKCFSRGDSVYCKDD 54
>gnl|CDD|188766 cd09380, LIM1_Lhx6, The first LIM domain of Lhx6. The first LIM
domain of Lhx6. Lhx6 is a member of LHX protein family,
which features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as
transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs such as the pituitary gland and the pancreas.
Lhx6 functions in the brain and nervous system. It is
expressed at high levels in several regions of the
embryonic mouse CNS, including the telencephalon and
hypothalamus, and the first branchial arch. Lhx6 is
proposed to have a role in patterning of the mandible
and maxilla, and in signaling during odontogenesis. In
brain sections, knockdown of Lhx6 gene blocks the
normal migration of neurons to the cortex. As in other
LIM domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 54
Score = 45.4 bits (107), Expect = 3e-07
Identities = 21/55 (38%), Positives = 36/55 (65%), Gaps = 1/55 (1%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
C CG +I D+Y+L+V +L WH CL C+ C L ++ +C++++ + +CK DY
Sbjct: 1 CSSCGLEILDRYLLKVN-NLIWHVRCLECSVCRTSLRQHNSCYIKNKEIFCKMDY 54
Score = 26.9 bits (59), Expect = 1.3
Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 1/55 (1%)
Query: 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKDDH 151
C C L + ++++ N I+HV+C C VC L + ++ +FCK D+
Sbjct: 1 CSSCGLEIL-DRYLLKVNNLIWHVRCLECSVCRTSLRQHNSCYIKNKEIFCKMDY 54
>gnl|CDD|188768 cd09382, LIM2_Lhx6, The second LIM domain of Lhx6. The second LIM
domain of Lhx6. Lhx6 is a member of LHX protein family,
which features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as transcription
factors or cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs such as the
pituitary gland and the pancreas. Lhx6 functions in
brain and nervous system. It is expressed at high
levels in several regions of the embryonic mouse CNS,
including the telencephalon and hypothalamus, and the
first branchial arch. Lhx6 is proposed to have a role in
patterning of the mandible and maxilla, and in signaling
during odontogenesis. In brain sections, knockdown of
Lhx6 gene blocks the normal migration of neurons to the
cortex. As in other LIM domains, this domain family is
50-60 amino acids in size and shares two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 55
Score = 45.1 bits (106), Expect = 4e-07
Identities = 20/52 (38%), Positives = 29/52 (55%)
Query: 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCK 148
C +C D+V RA+ YH+ CF C C +QL G+EF L E+ + C+
Sbjct: 1 CARCGRQIYASDWVRRARGNAYHLACFACFSCKRQLSTGEEFGLVEEKVLCR 52
Score = 25.0 bits (54), Expect = 5.9
Identities = 16/55 (29%), Positives = 23/55 (41%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
C CG QI+ +R A +H AC C C + L + + K C+ Y
Sbjct: 1 CARCGRQIYASDWVRRARGNAYHLACFACFSCKRQLSTGEEFGLVEEKVLCRIHY 55
>gnl|CDD|188750 cd09364, LIM1_LIMK, The first LIM domain of LIMK (LIM domain
Kinase ). The first LIM domain of LIMK (LIM domain
Kinase ): LIMK protein family is comprised of two
members LIMK1 and LIMK2. LIMK contains two LIM domains,
a PDZ domain and a kinase domain. LIMK is involved in
the regulation of actin polymerization and microtubule
disassembly. LIMK influences architecture of the actin
cytoskeleton by regulating the activity of the cofilin
family proteins cofilin1, cofilin2, and destrin. The
mechanism of the activation is to phosphorylates
cofilin on serine 3 and inactivates its actin-severing
activity, and altering the rate of actin
depolymerisation. LIMKs can function in both cytoplasm
and nucleus and are expressed in all tissues. Both
LIMK1 and LIMK2 can act in the nucleus to suppress
Rac/Cdc42-dependent cyclin D1 expression. However,
LIMK1 and LIMk2 have different cellular locations.
While LIMK1 localizes mainly at focal adhesions, LIMK2
is found in cytoplasmic punctae, suggesting that they
may have different cellular functions. The LIM domains
of LIMK have been shown to play an important role in
regulating kinase activity and likely also contribute
to LIMK function by acting as sites of
protein-to-protein interactions. All LIM domains are
50-60 amino acids in size and share two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 53
Score = 43.6 bits (103), Expect = 1e-06
Identities = 22/55 (40%), Positives = 31/55 (56%), Gaps = 3/55 (5%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
C GC G+I D ++ A + +WH C RC+ C L F +DGK YC++DY
Sbjct: 1 CAGCRGKILDSQYVQ-ALNQDWHCDCFRCSVCSDSLSN--WYFEKDGKLYCRKDY 52
Score = 24.8 bits (54), Expect = 8.9
Identities = 12/45 (26%), Positives = 24/45 (53%), Gaps = 2/45 (4%)
Query: 107 EDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKDDH 151
+ ++A N+ +H CF C VC L + + ++ L+C+ D+
Sbjct: 10 DSQYVQALNQDWHCDCFRCSVCSDSL--SNWYFEKDGKLYCRKDY 52
>gnl|CDD|188846 cd09462, LIM1_LIMK1, The first LIM domain of LIMK1 (LIM domain
Kinase 1). The first LIM domain of LIMK1 (LIM domain
Kinase 1): LIMK1 belongs to the LIMK protein family,
which comprises LIMK1 and LIMK2. LIMK contains two LIM
domains, a PDZ domain, and a kinase domain. LIMK is
involved in the regulation of actin polymerization and
microtubule disassembly. LIMK influences architecture
of the actin cytoskeleton by regulating the activity of
the cofilin family proteins cofilin1, cofilin2, and
destrin. The mechanism of the activation is to
phosphorylates cofilin on serine 3 and inactivates its
actin-severing activity, and altering the rate of actin
depolymerization. LIMKs can function in both cytoplasm
and nucleus. Both LIMK1 and LIMK2 can act in the
nucleus to suppress Rac/Cdc42-dependent cyclin D1
expression. LIMK1 is expressed in all tissues and is
localized to focal adhesions in the cell. LIMK1 can
form homodimers upon binding of HSP90 and is activated
by Rho effector Rho kinase and MAPKAPK2. LIMK1 is
important for normal central nervous system
development, and its deletion has been implicated in
the development of the human genetic disorder Williams
syndrome. Moreover, LIMK1 up-regulates the promoter
activity of urokinase type plasminogen activator and
induces its mRNA and protein expression in breast
cancer cells. The LIM domains have been shown to play
an important role in regulating kinase activity and
likely also contribute to LIMK function by acting as
sites of protein-to-protein interactions. All LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 74
Score = 44.1 bits (104), Expect = 1e-06
Identities = 23/58 (39%), Positives = 33/58 (56%), Gaps = 3/58 (5%)
Query: 4 LSLCVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
L +C CG I+D L+ A + +WHA C RC EC L + +DG+ +CK+DY
Sbjct: 19 LPVCASCGQSIYDGQYLQ-ALNSDWHADCFRCCECGASLSHW--YYEKDGRLFCKKDY 73
>gnl|CDD|188847 cd09463, LIM1_LIMK2, The first LIM domain of LIMK2 (LIM domain
Kinase 2). The first LIM domain of LIMK2 (LIM domain
Kinase 2): LIMK2 is a member of the LIMK protein
family, which comprises LIMK1 and LIMK2. LIMK contains
two LIM domains, a PDZ domain, and a kinase domain.
LIMK is involved in the regulation of actin
polymerization and microtubule disassembly. LIMK
influences architecture of the actin cytoskeleton by
regulating the activity of the cofilin family proteins
cofilin1, cofilin2, and destrin. The mechanism of the
activation is to phosphorylates cofilin on serine 3 and
inactivates its actin-severing activity, altering the
rate of actin depolymerization. LIMK activity is
activated by phosphorylation of a threonine residue
within the activation loop of the kinase by
p21-activated kinases 1 and 4 and by Rho kinase. LIMKs
can function in both cytoplasm and nucleus. Both LIMK1
and LIMK2 can act in the nucleus to suppress
Rac/Cdc42-dependent cyclin D1 expression. LIMK2 is
expressed in all tissues. While LIMK1 localizes mainly
at focal adhesions, LIMK2 is found in cytoplasmic
punctae, suggesting that they may have different
cellular functions. The activity of LIM kinase 2 to
regulate cofilin phosphorylation is inhibited by the
direct binding of Par-3. LIMK2 activation promotes cell
cycle progression. The phenotype of Limk2 knockout mice
shows a defect in spermatogenesis. The LIM domains have
been shown to play an important role in regulating
kinase activity and likely also contribute to LIMK
function by acting as sites of protein-to-protein
interactions. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 53
Score = 41.8 bits (98), Expect = 5e-06
Identities = 21/55 (38%), Positives = 30/55 (54%), Gaps = 3/55 (5%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
C GCGG+I D + RV + WH +C +C+ C L + +DGK YC + Y
Sbjct: 1 CTGCGGRIQDSFHYRVVQE-AWHNSCFQCSVCQDLLTN--WYYEKDGKLYCHKHY 52
>gnl|CDD|188715 cd09329, LIM3_abLIM, The third LIM domain of actin binding LIM
(abLIM) proteins. The third LIM domain of actin
binding LIM (abLIM) proteins: Three homologous members
of the abLIM protein family have been identified;
abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM
consists of four tandem repeats of LIM domains and the
C-terminal of acting binding LIM protein is a villin
headpiece domain, which has strong actin binding
activity. The abLIM-1, which is expressed in retina,
brain, and muscle tissue, has been indicated to
function as a tumor suppressor. AbLIM-2 and -3, mainly
expressed in muscle and neuronal tissue, bind to
F-actin strongly. They may serve as a scaffold for
signaling modules of the actin cytoskeleton and thereby
modulate transcription. It has shown that LIM domains
of abLIMs interact with STARS (striated muscle
activator of Rho signaling), which directly binds actin
and stimulates serum-response factor (SRF)-dependent
transcription. All LIM domains are 50-60 amino acids in
size and share two characteristic highly conserved zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 52
Score = 41.2 bits (97), Expect = 8e-06
Identities = 23/55 (41%), Positives = 31/55 (56%), Gaps = 3/55 (5%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
C GCG +I + L +A D +WH C +C EC + L +DGK YC+RDY
Sbjct: 1 CAGCGQEIKNGQAL-LALDKQWHVWCFKCKECGKVLTGEYMG--KDGKPYCERDY 52
>gnl|CDD|188775 cd09389, LIM2_LMO1_LMO3, The second LIM domain of LMO1 and LMO3
(LIM domain only protein 1 and 3). The second LIM
domain of LMO1 and LMO3 (LIM domain only protein 1 and
3): LMO1 and LMO3 are highly homologous and belong to
the LMO protein family. LMO1 and LMO3 are nuclear
protein that plays important roles in transcriptional
regulation and development. As LIM domains lack
intrinsic DNA-binding activity, nuclear LMOs are
involved in transcriptional regulation by forming
complexes with other transcription factors or cofactors.
For example, LMO1 interacts with the the bHLH domain of
bHLH transcription factor, TAL1 (T-cell acute
leukemia1)/SCL (stem cell leukemia) . LMO1 inhibits the
expression of TAL1/SCL target genes. LMO3 facilitates
p53 binding to its response elements, which suggests
that LMO3 acts as a co-repressor of p53, suppressing
p53-dependent transcriptional regulation. In addition,
LMO3 interacts with neuronal transcription factor, HEN2,
and acts as an oncogene in neuroblastoma. Another
binding partner of LMO3 is calcium- and integrin-binding
protein CIB, which binds via the second LIM domain
(LIM2) of LMO3. One role of the CIB/LMO3 complex is to
inhibit cell proliferation. Although LMO1 and LMO3 are
highly homologous proteins, they play different roles in
the regulation of the pituitary glycoprotein hormone
alpha-subunit (alpha GSU) gene. Alpha GSU promoter
activity was markedly repressed by LMO1 but activated by
LMO3. All LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 55
Score = 40.8 bits (95), Expect = 1e-05
Identities = 19/55 (34%), Positives = 33/55 (60%)
Query: 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKDDH 151
C C+ + VMRAK+ +YH+ CF C +C ++ GD+F L+ + + C+ D+
Sbjct: 1 CAACSKLIPAFEMVMRAKDNVYHLDCFACQLCNQRFCVGDKFFLKNNMILCQMDY 55
>gnl|CDD|188776 cd09390, LIM2_dLMO, The second LIM domain of dLMO (Beaderx). The
second LIM domain of dLMO (Beaderx): dLMO is a nuclear
protein that plays important roles in transcriptional
regulation and development. In Drosophila dLMO modulates
the activity of LIM-homeodomain protein Apterous (Ap),
which regulates the formation of the dorsal-ventral axis
of the Drosophila wing. Biochemical analysis shows that
dLMO protein influences the activity of Apterous by
binding of its cofactor Chip. Further studies shown that
dLMO proteins might function in an evolutionarily
conserved mechanism involved in patterning the
appendages. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 55
Score = 40.6 bits (95), Expect = 1e-05
Identities = 19/55 (34%), Positives = 30/55 (54%)
Query: 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKDDH 151
C C+ + VMRA+ +YH++CF C C + GD F L E+ + C+ D+
Sbjct: 1 CAACSKTIPAFEMVMRARTNVYHLECFACQRCNHRFCVGDRFYLCENKILCEYDY 55
>gnl|CDD|188771 cd09385, LIM2_LMO2, The second LIM domain of LMO2 (LIM domain only
protein 2). The second LIM domain of LMO2 (LIM domain
only protein 2): LMO2 is a nuclear protein that plays
important roles in transcriptional regulation and
development. The two tandem LIM domains of LMO2 support
the assembly of a crucial cell-regulatory complex by
interacting with both the TAL1-E47 and GATA1
transcription factors to form a DNA-binding complex that
is capable of transcriptional activation. LMOs have also
been shown to be involved in oncogenesis. LMO1 and LMO2
are activated in T-cell acute lymphoblastic leukemia by
distinct chromosomal translocations. LMO2 was also shown
to be involved in erythropoiesis and is required for the
hematopoiesis in the adult animals. All LIM domains are
50-60 amino acids in size and share two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 56
Score = 40.8 bits (95), Expect = 2e-05
Identities = 18/54 (33%), Positives = 28/54 (51%)
Query: 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKDD 150
C C+ + + MR K+K+YH++CF C C K GD + L + C+ D
Sbjct: 1 CASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQD 54
>gnl|CDD|188798 cd09414, LIM1_LIMPETin, The first LIM domain of protein LIMPETin.
The first LIM domain of protein LIMPETin: LIMPETin
contains 6 LIM domains at the C-terminal and an
N-terminal PET domain. Four of the six LIM domains are
highly homologous to the four and half LIM domain
protein family and two of them show sequence similarity
to the LIM domains of the Testin family. Thus, LIMPETin
may be the recombinant product of genes coding testin
and FHL proteins. In Schistosoma mansoni, where
LIMPETin was first identified, LIMPETin is down
regulated in sexually mature adult Schistosoma females
compared to sexually immature adult females and adult
male. Its differential expression indicates that it is
a transcription regulator. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 58
Score = 38.5 bits (90), Expect = 9e-05
Identities = 21/59 (35%), Positives = 28/59 (47%), Gaps = 5/59 (8%)
Query: 7 CVGCGGQIHDQYILRVAP----DLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
C GC + + AP L WH AC RC+ C + L + C V D + YC+R Y
Sbjct: 1 CGGCSEPLKYGELAVTAPKFGESLLWHPACFRCSTCEELLVDLTYC-VHDDQIYCERHY 58
>gnl|CDD|188774 cd09388, LIM1_LMO1_LMO3, The first LIM domain of LMO1 and LMO3
(LIM domain only protein 1 and 3). The first LIM
domain of LMO1 and LMO3 (LIM domain only protein 1 and
3): LMO1 and LMO3 are highly homologous and belong to
the LMO protein family. LMO1 and LMO3 are nuclear
protein that plays important roles in transcriptional
regulation and development. As LIM domains lack
intrinsic DNA-binding activity, nuclear LMOs are
involved in transcriptional regulation by forming
complexes with other transcription factors or
cofactors. For example, LMO1 interacts with the the
bHLH domain of bHLH transcription factor, TAL1 (T-cell
acute leukemia1)/SCL (stem cell leukemia) . LMO1
inhibits the expression of TAL1/SCL target genes. LMO3
facilitates p53 binding to its response elements, which
suggests that LMO3 acts as a co-repressor of p53,
suppressing p53-dependent transcriptional regulation.
In addition, LMO3 interacts with neuronal transcription
factor, HEN2, and acts as an oncogene in neuroblastoma.
Another binding partner of LMO3 is calcium- and
integrin-binding protein CIB, which binds via the
second LIM domain (LIM2) of LMO3. One role of the
CIB/LMO3 complex is to inhibit cell proliferation.
Although LMO1 and LMO3 are highly homologous proteins,
they play different roles in the regulation of the
pituitary glycoprotein hormone alpha-subunit (alpha
GSU) gene. Alpha GSU promoter activity was markedly
repressed by LMO1 but activated by LMO3. All LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 55
Score = 37.9 bits (88), Expect = 2e-04
Identities = 23/56 (41%), Positives = 31/56 (55%), Gaps = 2/56 (3%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDE-NCTCFVRDGKTYCKRDY 61
C GC +I D+Y+L+ A D WH CL+CA C L E T + + C+RDY
Sbjct: 1 CAGCNRKIKDRYLLK-ALDQYWHEDCLKCACCDCRLGEVGSTLYTKANLILCRRDY 55
>gnl|CDD|188770 cd09384, LIM1_LMO2, The first LIM domain of LMO2 (LIM domain only
protein 2). The first LIM domain of LMO2 (LIM domain
only protein 2): LMO2 is a nuclear protein that plays
important roles in transcriptional regulation and
development. The two tandem LIM domains of LMO2 support
the assembly of a crucial cell-regulatory complex by
interacting with both the TAL1-E47 and GATA1
transcription factors to form a DNA-binding complex
that is capable of transcriptional activation. LMOs
have also been shown to be involved in oncogenesis.
LMO1 and LMO2 are activated in T-cell acute
lymphoblastic leukemia by distinct chromosomal
translocations. LMO2 was also shown to be involved in
erythropoiesis and is required for the hematopoiesis in
the adult animals. All LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 56
Score = 37.5 bits (87), Expect = 2e-04
Identities = 22/57 (38%), Positives = 29/57 (50%), Gaps = 2/57 (3%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDE-NCTCFVRDGKTYCKRDYV 62
C GC I D+Y L+ A D WH CL C C L E + + G+ C+RDY+
Sbjct: 1 CGGCQQNIGDRYFLK-AIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYL 56
>gnl|CDD|188740 cd09354, LIM2_LPP, The second LIM domain of lipoma preferred
partner (LPP). The second LIM domain of lipoma
preferred partner (LPP): LPP is a member of the zyxin
LIM protein family and contains three LIM zinc-binding
domains at the C-terminal and proline-rich region at the
N-terminal. LPP initially identified as the most
frequent translocation partner of HMGA2 (High Mobility
Group A2) in a subgroup of benign tumors of adipose
tissue (lipomas). It was also shown to be rearranged in
a number of other soft tissues, as well as in a case of
acute monoblastic leukemia. In addition to its
involvement in tumors, LPP was inedited as a smooth
muscle restricted LIM protein that plays an important
role in SMC migration. LPP is localized at sites of cell
adhesion, cell-cell contacts and transiently in the
nucleus. In nucleus, it acts as a coactivator for the
ETS domain transcription factor PEA3. In addition to
PEA3, it interacts with alpha-actinin,vasodilator
stimulated phosphoprotein (VASP),Palladin, and Scrib.
The LIM domains are the main focal adhesion targeting
elements and that the proline- rich region, which
harbors binding sites for alpha-actinin and vasodilator-
stimulated phosphoprotein (VASP), has a weak targeting
capacity. As in other LIM domains, this domain family is
50-60 amino acids in size and shares two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 60
Score = 37.5 bits (87), Expect = 2e-04
Identities = 16/25 (64%), Positives = 18/25 (72%)
Query: 108 DFVMRAKNKIYHVQCFCCVVCGKQL 132
D ++RA K YH QCF CVVCGK L
Sbjct: 10 DRILRATGKPYHPQCFTCVVCGKSL 34
>gnl|CDD|188713 cd09327, LIM1_abLIM, The first LIM domain of actin binding LIM
(abLIM) proteins. The first LIM domain of actin binding
LIM (abLIM) proteins: Three homologous members of the
abLIM protein family have been identified; abLIM-1,
abLIM-2 and abLIM-3. The N-terminal of abLIM consists of
four tandem repeats of LIM domains and the C-terminal of
acting binding LIM protein is a villin headpiece domain,
which has strong actin binding activity. The abLIM-1,
which is expressed in retina, brain, and muscle tissue,
has been indicated to function as a tumor suppressor.
AbLIM-2 and -3, mainly expressed in muscle and neuronal
tissue, bind to F-actin strongly. They may serve as a
scaffold for signaling modules of the actin cytoskeleton
and thereby modulate transcription. It has shown that
LIM domains of abLIMs interact with STARS (striated
muscle activator of Rho signaling), which directly binds
actin and stimulates serum-response factor
(SRF)-dependent transcription. All LIM domains are 50-60
amino acids in size and share two characteristic highly
conserved zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 52
Score = 36.9 bits (86), Expect = 3e-04
Identities = 22/54 (40%), Positives = 30/54 (55%), Gaps = 3/54 (5%)
Query: 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKDD 150
C KC K E V+R ++K +H++CF C VCG L G F +E +C DD
Sbjct: 1 CYKCGKKCKGE--VLRVQDKYFHIKCFTCKVCGCDLAQGGFFV-KEGEYYCTDD 51
>gnl|CDD|188726 cd09340, LIM1_Testin_like, The first LIM domain of Testin-like
family. The first LIM domain of Testin_like family:
This family includes testin, prickle, dyxin and
LIMPETin. Structurally, testin and prickle proteins
contain three LIM domains at C-terminal; LIMPETin has
six LIM domains; and dyxin presents only two LIM
domains. However, all members of the family contain a
PET protein-protein interaction domain. Testin is a
cytoskeleton associated focal adhesion protein that
localizes along actin stress fibers, at
cell-cell-contact areas, and at focal adhesion plaques.
Testin interacts with a variety of cytoskeletal
proteins, including zyxin, mena, VASP, talin, and actin
and it is involved in cell motility and adhesion
events. Prickles have been implicated in roles of
regulating tissue polarity or planar cell polarity
(PCP). Dyxin involves in lung and heart development by
interaction with GATA6 and blocking GATA6 activated
target genes. LIMPETin might be the recombinant product
of genes coding testin and four and half LIM proteins
and its function is not well understood. As in other
LIM domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 58
Score = 37.2 bits (87), Expect = 3e-04
Identities = 19/59 (32%), Positives = 25/59 (42%), Gaps = 5/59 (8%)
Query: 7 CVGCGGQIH-DQYIL---RVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
C C I+ + + R D WH C C C++ L + F DGK YC R Y
Sbjct: 1 CEKCKEPINPGEVAVFAERAGEDACWHPGCFVCETCNELLVDL-IYFYHDGKIYCGRHY 58
Score = 30.3 bits (69), Expect = 0.081
Identities = 14/41 (34%), Positives = 19/41 (46%), Gaps = 4/41 (9%)
Query: 97 CEKCNLNFKRED---FVMRA-KNKIYHVQCFCCVVCGKQLV 133
CEKC + F RA ++ +H CF C C + LV
Sbjct: 1 CEKCKEPINPGEVAVFAERAGEDACWHPGCFVCETCNELLV 41
>gnl|CDD|188735 cd09349, LIM1_Zyxin, The first LIM domain of Zyxin. The first LIM
domain of Zyxin: Zyxin exhibits three copies of the LIM
domain, an extensive proline-rich domain and a nuclear
export signal. Localized at sites of cell substratum
adhesion in fibroblasts, Zyxin interacts with
alpha-actinin, members of the cysteine-rich protein
(CRP) family, proteins that display Src homology 3 (SH3)
domains and Ena/VASP family members. Zyxin and its
partners have been implicated in the spatial control of
actin filament assembly as well as in pathways important
for cell differentiation. In addition to its functions
at focal adhesion plaques, recent work has shown that
zyxin moves from the sites of cell contacts to the
nucleus, where it directly participates in the
regulation of gene expression. As in other LIM domains,
this domain family is 50-60 amino acids in size and
shares two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 87
Score = 37.5 bits (87), Expect = 4e-04
Identities = 17/53 (32%), Positives = 25/53 (47%), Gaps = 1/53 (1%)
Query: 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKD 149
C C R +RA ++HV CF C C +QL G +F E +C++
Sbjct: 34 CGICGQPLSRTQPAVRALGHLFHVTCFTCHQCEQQL-QGQQFYSLEGKPYCEE 85
>gnl|CDD|188714 cd09328, LIM2_abLIM, The second LIM domain on actin binding LIM
(abLIM) proteins. The second LIM domain of actin
binding LIM (abLIM) proteins: Three homologous members
of the abLIM protein family have been identified;
abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM
consists of four tandem repeats of LIM domains and the
C-terminal of acting binding LIM protein is a villin
headpiece domain, which has strong actin binding
activity. The abLIM-1, which is expressed in retina,
brain, and muscle tissue, has been indicated to function
as a tumor suppressor. AbLIM-2 and -3, mainly expressed
in muscle and neuronal tissue, bind to F-actin strongly.
They may serve as a scaffold for signaling modules of
the actin cytoskeleton and thereby modulate
transcription. It has shown that LIM domains of abLIMs
interact with STARS (striated muscle activator of Rho
signaling), which directly binds actin and stimulates
serum-response factor (SRF)-dependent transcription. All
LIM domains are 50-60 amino acids in size and share two
characteristic highly conserved zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 56
Score = 35.8 bits (83), Expect = 0.001
Identities = 19/43 (44%), Positives = 24/43 (55%), Gaps = 2/43 (4%)
Query: 94 GTKCEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGD 136
GTKC+ C + E V+ A K YH +CF C VC + PGD
Sbjct: 1 GTKCDSCQDFVEGE--VVSALGKTYHPKCFVCSVCRQPFPPGD 41
>gnl|CDD|188722 cd09336, LIM1_Paxillin_like, The first LIM domain of the paxillin
like protein family. The first LIM domain of the
paxillin like protein family: This family consists of
paxillin, leupaxin, Hic-5 (ARA55), and other related
proteins. There are four LIM domains in the C-terminal
of the proteins and leucine-rich LD-motifs in the
N-terminal region. Members of this family are adaptor
proteins to recruit key components of
signal-transduction machinery to specific sub-cellular
locations. Paxillin is found at the interface between
the plasma membrane and the actin cytoskeleton.
Paxillin serves as a platform for the recruitment of
numerous regulatory and structural proteins that
together control the dynamic changes in cell adhesion,
cytoskeletal reorganization and gene expression that
are necessary for cell migration and survival. Leupaxin
is a cytoskeleton adaptor protein, which is
preferentially expressed in hematopoietic cells. It
associates with focal adhesion kinases PYK2 and
pp125FAK and identified to be a component of the
osteoclast pososomal signaling complex. Hic-5 controls
cell proliferation, migration and senescence by
functioning as coactivator for steroid receptors such
as androgen receptor, glucocorticoid receptor and
progesterone receptor. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 53
Score = 34.6 bits (80), Expect = 0.002
Identities = 20/55 (36%), Positives = 24/55 (43%), Gaps = 3/55 (5%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
C C I Q + A WH CAEC L F RDG+ YC++DY
Sbjct: 1 CAACKKPIVGQVV--TALGKTWHPEHFVCAECKTELGTK-NFFERDGQPYCEKDY 52
>gnl|CDD|188744 cd09358, LIM_Mical_like, The LIM domain of Mical (molecule
interacting with CasL) like family. The LIM domain of
Mical (molecule interacting with CasL) like family:
Known members of this family includes LIM domain
containing proteins; Mical (molecule interacting with
CasL), pollen specific protein SF3, Eplin, xin
actin-binding repeat-containing protein 2 (XIRP2) and
Ltd-1. The members of this family function mainly at the
cytoskeleton and focal adhesions. They interact with
transcription factors or other signaling molecules to
play roles in muscle development, neuronal
differentiation, cell growth and mobility. Eplin has
also found to be tumor suppressor. As in other LIM
domains, this domain family is 50-60 amino acids in size
and shares two characteristic zinc finger motifs.. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 53
Score = 34.6 bits (80), Expect = 0.003
Identities = 15/38 (39%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 111 MRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCK 148
+ A K++H CF C C K L G +A E L+CK
Sbjct: 14 LVADGKLFHKSCFRCSHCNKTLRLG-NYASLEGKLYCK 50
>gnl|CDD|188724 cd09338, LIM3_Paxillin_like, The third LIM domain of the paxillin
like protein family. The third LIM domain of the
paxillin like protein family: This family consists of
paxillin, leupaxin, Hic-5 (ARA55), and other related
proteins. There are four LIM domains in the C-terminal
of the proteins and leucine-rich LD-motifs in the
N-terminal region. Members of this family are adaptor
proteins to recruit key components of
signal-transduction machinery to specific sub-cellular
locations. Paxillin is found at the interface between
the plasma membrane and the actin cytoskeleton.
Paxillin serves as a platform for the recruitment of
numerous regulatory and structural proteins that
together control the dynamic changes in cell adhesion,
cytoskeletal reorganization and gene expression that
are necessary for cell migration and survival. Leupaxin
is a cytoskeleton adaptor protein, which is
preferentially expressed in hematopoietic cells. It
associates with focal adhesion kinases PYK2 and
pp125FAK and identified to be a component of the
osteoclast pososomal signaling complex. Hic-5 controls
cell proliferation, migration and senescence by
functioning as coactivator for steroid receptors such
as androgen receptor, glucocorticoid receptor and
progesterone receptor. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 53
Score = 34.2 bits (79), Expect = 0.003
Identities = 20/55 (36%), Positives = 27/55 (49%), Gaps = 3/55 (5%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
C GC I + YI A + +WH C C ECH+ N + F +G YC+ Y
Sbjct: 1 CGGCNKPILENYI--SALNTQWHPECFVCRECHKPF-INGSFFEHEGLPYCETHY 52
>gnl|CDD|188758 cd09372, LIM2_FBLP-1, The second LIM domain of the filamin-binding
LIM protein-1 (FBLP-1). The second LIM domain of the
filamin-binding LIM protein-1 (FBLP-1): Fblp-1 contains
a proline-rich domain near its N terminus and two LIM
domains at its C terminus. FBLP-1 mRNA was detected in a
variety of tissues and cells including platelets and
endothelial cells. FBLP-1 binds to Filamins. The
association between filamin B and FBLP-1 may play an
unknown role in cytoskeletal function, cell adhesion,
and cell motility. As in other LIM domains, this domain
family is 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein.
Length = 53
Score = 33.9 bits (78), Expect = 0.003
Identities = 23/56 (41%), Positives = 32/56 (57%), Gaps = 6/56 (10%)
Query: 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDE-FALREDG-LFCKDD 150
C KC + ++RA K YH CF CV CG+++ GDE FA+ E ++C DD
Sbjct: 1 CAKCQGVIT--EHIIRALGKGYHPPCFTCVTCGRRI--GDESFAVDEQNEVYCLDD 52
>gnl|CDD|188791 cd09407, LIM2_Paxillin, The second LIM domain of paxillin. The
second LIM domain of paxillin: Paxillin is an adaptor
protein, which recruits key components of the
signal-transduction machinery to specific sub-cellular
locations to respond to environmental changes rapidly.
The C-terminal region of paxillin contains four LIM
domains which target paxillin to focal adhesions,
presumably through a direct association with the
cytoplasmic tail of beta-integrin. The N-terminal of
paxillin is leucine-rich LD-motifs. Paxillin is found
at the interface between the plasma membrane and the
actin cytoskeleton. The binding partners of paxillin
are diverse and include protein tyrosine kinases, such
as Src and FAK, structural proteins, such as vinculin
and actopaxin, and regulators of actin organization.
Paxillin recruits these proteins to their function
sites to control the dynamic changes in cell adhesion,
cytoskeletal reorganization and gene expression. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 52
Score = 33.4 bits (76), Expect = 0.006
Identities = 20/55 (36%), Positives = 26/55 (47%), Gaps = 3/55 (5%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
C C G I D+ + A D WH CA+C F +DGK YC++DY
Sbjct: 1 CYYCNGPILDKVV--TALDRTWHPEHFFCAQCGAFFGPE-GFHEKDGKAYCRKDY 52
>gnl|CDD|188748 cd09362, LIM2_Enigma_like, The second LIM domain of Enigma-like
family. The second LIM domain of Enigma-like family:
The Enigma LIM domain family is comprised of three
members: Enigma, ENH, and Cypher (mouse)/ZASP (human).
These subfamily members contain a single PDZ domain at
the N-terminus and three LIM domains at the C-terminus.
Enigma was initially characterized in humans and is
expressed in multiple tissues, such as skeletal muscle,
heart, bone and brain. The third LIM domain
specifically interacts with the insulin receptor and
the second LIM domain interacts with the receptor
tyrosine kinase Ret and the adaptor protein APS. Thus
Enigma is implicated in signal transduction processes,
such as mitogenic activity, insulin related actin
organization, and glucose metabolism. The second
member, ENH protein, was first identified in rat brain.
It has been shown that ENH interacts with protein
kinase D1 (PKD1) via its LIM domains and forms a
complex with PKD1 and the alpha1C subunit of cardiac
L-type voltage-gated calcium channel in rat neonatal
cardiomyocytes. The N-terminal PDZ domain interacts
with alpha-actinin at the Z-line. ZASP/Cypher is
required for maintenance of Z-line structure during
muscle contraction, but not required for Z-line
assembly. In heart, Cypher/ZASP plays a structural role
through its interaction with cytoskeletal Z-line
proteins. In addition, there is increasing evidence
that Cypher/ZASP also performs signaling functions.
Studies reveal that Cypher/ZASP interacts with and
directs PKC to the Z-line, where PKC phosphorylates
downstream signaling targets. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 52
Score = 33.2 bits (76), Expect = 0.006
Identities = 14/34 (41%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 28 WHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
WH +C CA C Q + N + DG+ YC++DY
Sbjct: 20 WHVSCFVCAACKQPI-GNSLFHMEDGEPYCEKDY 52
Score = 27.4 bits (61), Expect = 0.93
Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 3/55 (5%)
Query: 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKDDH 151
C +C+ E VM A + +HV CF C C KQ + F + + +C+ D+
Sbjct: 1 CARCHKKILGE--VMHALKQTWHVSCFVCAAC-KQPIGNSLFHMEDGEPYCEKDY 52
>gnl|CDD|188737 cd09351, LIM1_LPP, The first LIM domain of lipoma preferred partner
(LPP). The first LIM domain of lipoma preferred partner
(LPP): LPP is a member of the zyxin LIM protein family
and contains three LIM zinc-binding domains at the
C-terminal and proline-rich region at the N-terminal.
LPP initially identified as the most frequent
translocation partner of HMGA2 (High Mobility Group A2)
in a subgroup of benign tumors of adipose tissue
(lipomas). It was also shown to be rearranged in a
number of other soft tissues, as well as in a case of
acute monoblastic leukemia. In addition to its
involvement in tumors, LPP was inedited as a smooth
muscle restricted LIM protein that plays an important
role in SMC migration. LPP is localized at sites of cell
adhesion, cell-cell contacts and transiently in the
nucleus. In nucleus, it acts as a coactivator for the
ETS domain transcription factor PEA3. In addition to
PEA3, it interacts with alpha-actinin,vasodilator
stimulated phosphoprotein (VASP),Palladin, and Scrib.
The LIM domains are the main focal adhesion targeting
elements and that the proline- rich region, which
harbors binding sites for alpha-actinin and vasodilator-
stimulated phosphoprotein (VASP), has a weak targeting
capacity. As in other LIM domains, this domain family is
50-60 amino acids in size and shares two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 54
Score = 33.6 bits (77), Expect = 0.007
Identities = 16/55 (29%), Positives = 25/55 (45%), Gaps = 1/55 (1%)
Query: 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKDDH 151
C KC E A +++YH+ CF C C L G F + +C++D+
Sbjct: 1 CVKCGEKVLGEGSGCTAMDQVYHISCFTCHQCQINL-QGKPFYALDGKPYCEEDY 54
Score = 27.0 bits (60), Expect = 1.3
Identities = 18/55 (32%), Positives = 27/55 (49%), Gaps = 1/55 (1%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
CV CG ++ + A D +H +C C +C L + + DGK YC+ DY
Sbjct: 1 CVKCGEKVLGEGSGCTAMDQVYHISCFTCHQCQINL-QGKPFYALDGKPYCEEDY 54
>gnl|CDD|188777 cd09391, LIM1_Lrg1p_like, The first LIM domain of Lrg1p, a LIM and
RhoGap domain containing protein. The first LIM domain
of Lrg1p, a LIM and RhoGap domain containing protein:
The members of this family contain three tandem repeats
of LIM domains and a Rho-type GTPase activating protein
(RhoGap) domain. Lrg1p is a Rho1 GTPase-activating
protein required for efficient cell fusion in yeast.
Lrg1p-GAP domain strongly and specifically stimulates
the GTPase activity of Rho1p, a regulator of beta
(1-3)-glucan synthase in vitro. The LIM domain is 50-60
amino acids in size and shares two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 57
Score = 33.4 bits (77), Expect = 0.007
Identities = 15/38 (39%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVP 134
C KC + FV RA +YH+ CF C CGK +
Sbjct: 1 CAKCGKPITGQ-FV-RALGDVYHLDCFTCHDCGKPVAS 36
>gnl|CDD|188717 cd09331, LIM1_PINCH, The first LIM domain of protein PINCH. The
first LIM domain of paxillin: Paxillin is an adaptor
protein, which recruits key components of the
signal-transduction machinery to specific sub-cellular
locations to respond to environmental changes rapidly.
The C-terminal region of paxillin contains four LIM
domains which target paxillin to focal adhesions,
presumably through a direct association with the
cytoplasmic tail of beta-integrin. The N-terminal of
paxillin is leucine-rich LD-motifs. Paxillin is found at
the interface between the plasma membrane and the actin
cytoskeleton. The binding partners of paxillin are
diverse and include protein tyrosine kinases, such as
Src and FAK, structural proteins, such as vinculin and
actopaxin, and regulators of actin organization.
Paxillin recruits these proteins to their function sites
to control the dynamic changes in cell adhesion,
cytoskeletal reorganization and gene expression. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 59
Score = 33.5 bits (77), Expect = 0.007
Identities = 16/54 (29%), Positives = 28/54 (51%), Gaps = 1/54 (1%)
Query: 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKDD 150
CE+C F+ ++ ++ + ++YH QCF C C + P F E +C+ D
Sbjct: 1 CERCREGFEPDEKIVNSNGELYHEQCFVCAQCFQPF-PDGLFYEFEGRKYCEHD 53
Score = 27.7 bits (62), Expect = 0.90
Identities = 10/34 (29%), Positives = 18/34 (52%), Gaps = 1/34 (2%)
Query: 28 WHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
+H C CA+C Q + + +G+ YC+ D+
Sbjct: 22 YHEQCFVCAQCFQPFPDG-LFYEFEGRKYCEHDF 54
>gnl|CDD|188799 cd09415, LIM1_Prickle, The first LIM domain of Prickle. The
first LIM domain of Prickle: Prickle contains three
C-terminal LIM domains and a N-terminal PET domain.
Prickles have been implicated in roles of regulating
tissue polarity or planar cell polarity (PCP). PCP
establishment requires the conserved
Frizzled/Dishevelled PCP pathway. Prickle interacts
with Dishevelled, thereby modulating
Frizzled/Dishevelled activity and PCP signaling. Four
forms of prickles have been identified: prickle 1-4.
The best characterized is prickle 1 and prickle 2 which
are differentially expressed. While prickle 1 is
expressed in fetal heart and hematological
malignancies, prickle 2 is found in fetal brain, adult
cartilage, pancreatic islet, and some types of timorous
cells. Mutations in prickle 1 have been linked to
progressive myoclonus epilepsy. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 59
Score = 33.4 bits (77), Expect = 0.007
Identities = 22/57 (38%), Positives = 26/57 (45%), Gaps = 5/57 (8%)
Query: 7 CVGCGGQIHDQYIL----RVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKR 59
C CG QI I R P WH AC C+ C + L + F +DGK YC R
Sbjct: 1 CEQCGEQISGGDIAVFASRAGPGACWHPACFVCSTCKELL-VDLIYFYQDGKVYCGR 56
>gnl|CDD|188783 cd09397, LIM1_UF1, LIM domain in proteins of unknown function.
The first Lim domain of a LIM domain containing
protein: The functions of the proteins are unknown. The
members of this family contain two copies of LIM
domain. The LIM domain is 50-60 amino acids in size and
shares two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to
two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric
protein.
Length = 58
Score = 33.0 bits (76), Expect = 0.009
Identities = 12/34 (35%), Positives = 16/34 (47%)
Query: 28 WHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
WH C C C + C+V D K YC++ Y
Sbjct: 24 WHRECFVCTTCGCPFQFSVPCYVLDDKPYCQQHY 57
>gnl|CDD|188867 cd09483, LIM1_Prickle_1, The first LIM domain of Prickle 1. The
first LIM domain of Prickle 1. Prickle contains three
C-terminal LIM domains and a N-terminal PET domain
Prickles have been implicated in roles of regulating
tissue polarity or planar cell polarity (PCP). PCP
establishment requires the conserved
Frizzled/Dishevelled PCP pathway. Prickle interacts
with Dishevelled, thereby modulating
Frizzled/Dishevelled activity and PCP signaling. Four
forms of prickles have been identified: prickle 1-4.
The best characterized is prickle 1 and prickle 2 which
are differentially expressed. While prickle 1 is
expressed in fetal heart and hematological
malignancies, prickle 2 is found in mainly expressed in
fetal brain, adult cartilage, pancreatic islet, and
some types of timorous cells. In addition, Prickle 1
regulates cell movements during gastrulation and
neuronal migration through interaction with the
noncanonical Wnt11/Wnt5 pathway in zebrafish. Mutations
in prickle 1 have been linked to progressive myoclonus
epilepsy. LIM domains are 50-60 amino acids in size
and share two characteristic zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 59
Score = 32.6 bits (74), Expect = 0.015
Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 5/59 (8%)
Query: 7 CVGCGGQIHDQ----YILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
C CG +I+ + R P + WH +C C C++ L + F +DGK +C R +
Sbjct: 1 CEQCGIKINGGEVAVFASRAGPGVCWHPSCFVCFTCNELL-VDLIYFYQDGKIHCGRHH 58
>gnl|CDD|188778 cd09392, LIM2_Lrg1p_like, The second LIM domain of Lrg1p, a LIM
and RhoGap domain containing protein. The second LIM
domain of Lrg1p, a LIM and RhoGap domain containing
protein: The members of this family contain three
tandem repeats of LIM domains and a Rho-type GTPase
activating protein (RhoGap) domain. Lrg1p is a Rho1
GTPase-activating protein required for efficient cell
fusion in yeast. Lrg1p-GAP domain strongly and
specifically stimulates the GTPase activity of Rho1p, a
regulator of beta (1-3)-glucan synthase in vitro. The
LIM domain is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein.
Length = 53
Score = 31.9 bits (73), Expect = 0.019
Identities = 16/55 (29%), Positives = 23/55 (41%), Gaps = 2/55 (3%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
C CGG + YI A ++H C+ C N + + +GK YC Y
Sbjct: 1 CFKCGGALRGSYI--TALGRKYHVEHFTCSVCPTVFGPNDSYYEHEGKIYCHYHY 53
Score = 30.8 bits (70), Expect = 0.062
Identities = 16/55 (29%), Positives = 23/55 (41%), Gaps = 2/55 (3%)
Query: 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKDDH 151
C KC R ++ K YHV+ F C VC P D + E ++C +
Sbjct: 1 CFKCG-GALRGSYITALGRK-YHVEHFTCSVCPTVFGPNDSYYEHEGKIYCHYHY 53
>gnl|CDD|188790 cd09406, LIM1_Leupaxin, The first LIM domain of Leupaxin. The
first LIM domain of Leupaxin: Leupaxin is a
cytoskeleton adaptor protein, which is preferentially
expressed in hematopoietic cells. Leupaxin belongs to
the paxillin focal adhesion protein family. Same as
other members of the family, it has four leucine-rich
LD-motifs in the N-terminus and four LIM domains in the
C-terminus. It may function in cell type-specific
signaling by associating with interaction partners
PYK2, FAK, PEP and p95PKL. When expressed in human
leukocytic cells, leupaxin significantly suppressed
integrin-mediated cell adhesion to fibronectin and the
tyrosine phosphorylation of paxillin. These findings
indicate that leupaxin may negatively regulate the
functions of paxillin during integrin signaling. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 55
Score = 32.1 bits (73), Expect = 0.020
Identities = 17/55 (30%), Positives = 24/55 (43%), Gaps = 3/55 (5%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
C C I Q + A WH C +C + L + F R+G+ YC+ DY
Sbjct: 3 CASCQKPIAGQVV--TALGQTWHPEHFVCCQCGKELG-SRPFFERNGQAYCEEDY 54
>gnl|CDD|188809 cd09425, LIM4_LIMPETin, The fourth LIM domain of protein LIMPETin.
The fourth LIM domain of protein LIMPETin: LIMPETin
contains 6 LIM domains at the C-terminal and an
N-terminal PET domain. Four of the six LIM domains are
highly homologous to the four and half LIM domain
protein family and two of them show sequence similarity
to the LIM domains of the Testin family. Thus, LIMPETin
may be the recombinant product of genes coding testin
and FHL proteins. In Schistosoma mansoni, where
LIMPETin was first identified, LIMPETin is down
regulated in sexually mature adult Schistosoma females
compared to sexually immature adult females and adult
male. Its differential expression indicates that it is a
transcription regulator. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 54
Score = 32.0 bits (73), Expect = 0.021
Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFC 147
C+ C F+ M K + +H +CFCC C KQ + F ++D ++C
Sbjct: 1 CDGCGEIFRAGMKKMEYKGQQWHEKCFCCCEC-KQPIGTKSFIPKDDDVYC 50
>gnl|CDD|188868 cd09484, LIM1_Prickle_2, The first LIM domain of Prickle 2. The
first LIM domain of Prickle 2: Prickle contains three
C-terminal LIM domains and a N-terminal PET domain.
Prickles have been implicated in roles of regulating
tissue polarity or planar cell polarity (PCP). PCP
establishment requires the conserved
Frizzled/Dishevelled PCP pathway. Prickle interacts
with Dishevelled, thereby modulating
Frizzled/Dishevelled activity and PCP signaling. Four
forms of prickles have been identified: prickle 1-4.
The best characterized is prickle 1 and prickle 2 which
are differentially expressed. While prickle 1 is
expressed in fetal heart and hematological
malignancies, prickle 2 is found in fetal brain, adult
cartilage, pancreatic islet, and some types of timorous
cells. Mutations in prickle 1 have been linked to
progressive myoclonus epilepsy. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 59
Score = 31.8 bits (72), Expect = 0.030
Identities = 20/59 (33%), Positives = 29/59 (49%), Gaps = 5/59 (8%)
Query: 7 CVGCGGQIHDQ----YILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
C CGGQI+ + R + WH C C+ C++ L + F +DGK YC R +
Sbjct: 1 CEQCGGQINGGDIAVFASRAGHGVCWHPQCFVCSVCNELL-VDLIYFYQDGKIYCGRHH 58
Score = 25.7 bits (56), Expect = 3.8
Identities = 21/60 (35%), Positives = 29/60 (48%), Gaps = 7/60 (11%)
Query: 97 CEKCNLNFKRED---FVMRAKNKI-YHVQCFCCVVCGKQLVPGDEFALREDG-LFCKDDH 151
CE+C D F RA + + +H QCF C VC + LV D +DG ++C H
Sbjct: 1 CEQCGGQINGGDIAVFASRAGHGVCWHPQCFVCSVCNELLV--DLIYFYQDGKIYCGRHH 58
>gnl|CDD|188787 cd09403, LIM2_CRP, The second LIM domain of Cysteine Rich Protein
(CRP). The second LIM domain of Cysteine Rich Protein
(CRP): Cysteine-rich proteins (CRPs) are characterized
by the presence of two LIM domains linked to a short
glycine-rich repeats (GRRs). The CRP family members
include CRP1, CRP2, CRP3/MLP. CRP1, CRP2 and CRP3 share
a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K),
which supports the fact that these proteins function
not only in the cytoplasm but also in the nucleus. CRPs
control regulatory pathways during cellular
differentiation, and involve in complex transcription
control, and the organization as well as the
arrangement of the myofibrillar/cytoskeletal network.
It is evident that CRP1, CRP2, and CRP3/MLP are
involved in promoting protein assembly along the
actin-based cytoskeleton. Although members of the CRP
family share common binding partners, they are also
capable of recognizing different and specific targets.
LIM domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residu es, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 54
Score = 31.4 bits (71), Expect = 0.033
Identities = 16/34 (47%), Positives = 21/34 (61%), Gaps = 1/34 (2%)
Query: 28 WHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
WH C RCA+C + L E+ T +DG+ YCK Y
Sbjct: 21 WHKNCFRCAKCGKSL-ESTTLADKDGEIYCKGCY 53
>gnl|CDD|188731 cd09345, LIM2_FHL, The second LIM domain of Four and a half LIM
domains protein (FHL). The second LIM domain of Four
and a half LIM domains protein (FHL): LIM-only protein
family consists of five members, designated FHL1, FHL2,
FHL3, FHL5 and LIMPETin. The first four members are
composed of four complete LIM domains arranged in tandem
and an N-terminal single zinc finger domain with a
consensus sequence equivalent to the C-terminal half of
a LIM domain. LIMPETin is an exception, containing six
LIM domains. FHL1, 2 and 3 are predominantly expressed
in muscle tissues, and FHL5 is highly expressed in male
germ cells. FHL proteins exert their roles as
transcription co-activators or co-repressors through a
wide array of interaction partners. For example, FHL1
binds to Myosin-binding protein C, regulating myosin
filament formation and sarcomere assembly. FHL2 has
shown to interact with more than 50 different proteins,
including receptors, structural proteins, transcription
factors and cofactors, signal transducers, splicing
factors, DNA replication and repair enzymes, and
metabolic enzymes. FHL3 int eracts with many
transcription factors, such as CREB, BKLF/KLF3, CtBP2,
MyoD, and MZF_1. FHL5 is a tissue-specific coactivator
of CREB/CREM family transcription factors. LIM domains
are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 54
Score = 31.5 bits (72), Expect = 0.033
Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 1/53 (1%)
Query: 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKD 149
C+ C M K K +H +CF C C K+ + F ++D ++C
Sbjct: 1 CKACGKAIMPGSKKMEYKGKFWHEKCFTCSEC-KKPIGTKSFIPKDDKIYCVP 52
>gnl|CDD|188712 cd09326, LIM_CRP_like, The LIM domains of Cysteine Rich Protein
(CRP) family. The LIM domains of Cysteine Rich Protein
(CRP) family: Cysteine-rich proteins (CRPs) are
characterized by the presence of two LIM domains linked
to a short glycine-rich repeats (GRRs). The known CRP
family members include CRP1, CRP2, and CRP3/MLP. CRP1,
CRP2 and CRP3 share a conserved nuclear targeting
signal (K/R-K/R-Y-G-P-K), which supports the fact that
these proteins function not only in the cytoplasm but
also in the nucleus. CRPs control regulatory pathways
during cellular differentiation, and involve in complex
transcription control, and the organization as well as
the arrangement of the myofibrillar/cytoskeletal
network. CRP1, CRP2, and CRP3/MLP are involved in
promoting protein assembly along the actin-based
cytoskeleton. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 53
Score = 31.0 bits (71), Expect = 0.041
Identities = 14/31 (45%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 28 WHAACLRCAECHQFLDENCTCFVRDGKTYCK 58
WH +C CA C++ LD T DG+ YCK
Sbjct: 21 WHKSCFTCAVCNKRLDST-TLAEHDGEIYCK 50
Score = 26.4 bits (59), Expect = 1.8
Identities = 13/38 (34%), Positives = 19/38 (50%), Gaps = 1/38 (2%)
Query: 111 MRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCK 148
+ A K +H CF C VC K+L A + ++CK
Sbjct: 14 VIAAGKSWHKSCFTCAVCNKRLDSTT-LAEHDGEIYCK 50
>gnl|CDD|188872 cd09841, LIM1_Prickle_3, The first LIM domain of Prickle 3. The
first LIM domain of Prickle 3/LIM domain only 6 (LM06):
Prickle contains three C-terminal LIM domains and a
N-terminal PET domain. Prickles have been implicated
in roles of regulating tissue polarity or planar cell
polarity (PCP). PCP establishment requires the
conserved Frizzled/Dishevelled PCP pathway. Prickle
interacts with Dishevelled, thereby modulating
Frizzled/Dishevelled activity and PCP signaling. Four
forms of prickles have been identified: prickle 1-4.
The best characterized is prickle 1 and prickle 2 which
are differentially expressed. While prickle 1 is
expressed in fetal heart and hematological
malignancies, prickle 2 is found in fetal brain, adult
cartilage, pancreatic islet, and some types of timorous
cells. Mutations in prickle 1 have been linked to
progressive myoclonus epilepsy. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 59
Score = 31.0 bits (70), Expect = 0.047
Identities = 21/57 (36%), Positives = 25/57 (43%), Gaps = 5/57 (8%)
Query: 7 CVGCGGQIHDQYIL----RVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKR 59
C CG QI I R WH C +CA C + L + F +DGK YC R
Sbjct: 1 CQQCGRQICGGDIAVFASRAGLGACWHPQCFQCASCQELL-VDLIYFYQDGKIYCGR 56
>gnl|CDD|188742 cd09356, LIM2_TRIP6, The second LIM domain of Thyroid
receptor-interacting protein 6 (TRIP6). The second LIM
domain of Thyroid receptor-interacting protein 6
(TRIP6): TRIP6 is a member of the zyxin LIM protein
family and contains three LIM zinc-binding domains at
the C-terminal. TRIP6 protein localizes to focal
adhesion sites and along actin stress fibers.
Recruitment of this protein to the plasma membrane
occurs in a lysophosphatidic acid (LPA)-dependent
manner. TRIP6 recruits a number of molecules involved in
actin assembly, cell motility, survival and
transcriptional control. The function of TRIP6 in cell
motility is regulated by Src-dependent phosphorylation
at a Tyr residue. The phosphorylation activates the
coupling to the Crk SH2 domain, which is required for
the function of TRIP6 in promoting lysophosphatidic acid
(LPA)-induced cell migration. TRIP6 can shuttle to the
nucleus to serve as a coactivator of AP-1 and NF-kappaB
transcriptional factors. Moreover, TRIP6 can form a
ternary complex with the NHERF2 PDZ protein and LPA2
receptor to regulate LPA-induced activation of ERK and
AKT, rendering cells resistant to chemotherapy. Recent
evidence shows that TRIP6 antagonizes Fas-Induced
apoptosis by enhancing the antiapoptotic effect of LPA
in cells. As in other LIM domains, this domain family is
50-60 amino acids in size and shares two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 53
Score = 31.0 bits (70), Expect = 0.050
Identities = 12/25 (48%), Positives = 16/25 (64%)
Query: 108 DFVMRAKNKIYHVQCFCCVVCGKQL 132
+ ++RA K YH CF CVVC + L
Sbjct: 10 ERILRATGKAYHPHCFTCVVCHRSL 34
>gnl|CDD|188723 cd09337, LIM2_Paxillin_like, The second LIM domain of the
paxillin like protein family. The second LIM domain of
the paxillin like protein family: This family consists
of paxillin, leupaxin, Hic-5 (ARA55), and other related
proteins. There are four LIM domains in the C-terminal
of the proteins and leucine-rich LD-motifs in the
N-terminal region. Members of this family are adaptor
proteins to recruit key components of
signal-transduction machinery to specific sub-cellular
locations. Paxillin is found at the interface between
the plasma membrane and the actin cytoskeleton.
Paxillin serves as a platform for the recruitment of
numerous regulatory and structural proteins that
together control the dynamic changes in cell adhesion,
cytoskeletal reorganization and gene expression that
are necessary for cell migration and survival. Leupaxin
is a cytoskeleton adaptor protein, which is
preferentially expressed in hematopoietic cells. It
associates with focal adhesion kinases PYK2 and
pp125FAK and identified to be a component of the
osteoclast pososomal signaling complex. Hic-5 controls
cell proliferation, migration and senescence by
functioning as coactivator for steroid receptors such
as androgen receptor, glucocorticoid receptor and
progesterone receptor. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 52
Score = 30.8 bits (70), Expect = 0.054
Identities = 19/55 (34%), Positives = 26/55 (47%), Gaps = 3/55 (5%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
C C G I D+ + A D WH CA+C + + +DGK YC+ DY
Sbjct: 1 CAYCNGPILDKCV--TALDKTWHPEHFFCAQCGKPFGDE-GFHEKDGKPYCREDY 52
Score = 28.5 bits (64), Expect = 0.37
Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 5/56 (8%)
Query: 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDE-FALREDGLFCKDDH 151
C CN D + A +K +H + F C CGK GDE F ++ +C++D+
Sbjct: 1 CAYCNGPIL--DKCVTALDKTWHPEHFFCAQCGKPF--GDEGFHEKDGKPYCREDY 52
>gnl|CDD|188840 cd09456, LIM2_Enigma, The second LIM domain of Enigma. The
second LIM domain of Enigma: Enigma was initially
characterized in humans as a protein containing three
LIM domains at the C-terminus and a PDZ domain at
N-terminus. The third LIM domain specifically
interacts with the insulin receptor and the second LIM
domain interacts with the receptor tyrosine kinase Ret
and the adaptor protein APS. Thus Enigma is implicated
in signal transduction processes, such as mitogenic
activity, insulin related actin organization, and
glucose metabolism. Enigma is expressed in multiple
tissues, such as skeletal muscle, heart, bone and
brain. LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to
two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 52
Score = 30.7 bits (69), Expect = 0.058
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 23 APDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
A + WH C CA C + N ++ +G YC+RDY
Sbjct: 15 ALKMTWHVHCFTCAACKTPI-RNRAFYMEEGAPYCERDY 52
Score = 28.0 bits (62), Expect = 0.51
Identities = 17/55 (30%), Positives = 24/55 (43%), Gaps = 3/55 (5%)
Query: 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKDDH 151
C KC E +M A +HV CF C C K + F + E +C+ D+
Sbjct: 1 CAKCKKKITGE--IMHALKMTWHVHCFTCAAC-KTPIRNRAFYMEEGAPYCERDY 52
>gnl|CDD|188793 cd09409, LIM3_Paxillin, The third LIM domain of paxillin. The
third LIM domain of paxillin: Paxillin is an adaptor
protein, which recruits key components of the
signal-transduction machinery to specific sub-cellular
locations to respond to environmental changes rapidly.
The C-terminal region of paxillin contains four LIM
domains which target paxillin to focal adhesions,
presumably through a direct association with the
cytoplasmic tail of beta-integrin. The N-terminal of
paxillin is leucine-rich LD-motifs. Paxillin is found
at the interface between the plasma membrane and the
actin cytoskeleton. The binding partners of paxillin
are diverse and include protein tyrosine kinases, such
as Src and FAK, structural proteins, such as vinculin
and actopaxin, and regulators of actin organization.
Paxillin recruits these proteins to their function
sites to control the dynamic changes in cell adhesion,
cytoskeletal reorganization and gene expression. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 53
Score = 30.2 bits (68), Expect = 0.079
Identities = 20/55 (36%), Positives = 25/55 (45%), Gaps = 3/55 (5%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
C GC I + YI A + WH C C EC N + F DG+ YC+ Y
Sbjct: 1 CGGCARAILENYI--SALNTLWHPECFVCRECFTPF-VNGSFFEHDGQPYCEAHY 52
>gnl|CDD|188871 cd09840, LIM2_CRP2, The second LIM domain of Cysteine Rich
Protein 2 (CRP2). The second LIM domain of Cysteine
Rich Protein 2 (CRP2): Cysteine-rich proteins (CRPs)
are characterized by the presence of two LIM domains
linked to short glycine-rich repeats (GRRs). The CRP
family members include CRP1, CRP2, CRP3/MLP and
TLPCRP1, CRP2 and CRP3 share a conserved nuclear
targeting signal (K/R-K/R-Y-G-P-K), which supports the
fact that these proteins function not only in the
cytoplasm but also in the nucleus. CRPs control
regulatory pathways during cellular differentiation,
and involve in complex transcription circuits, and the
organization as well as the arrangement of the
myofibrillar/cytoskeletal network.CRP3 also called
Muscle LIM Protein (MLP), which is a striated
muscle-specific factor that enhances myogenic
differentiation. The second LIM domain of CRP3/MLP
interacts with cytoskeletal protein beta-spectrin.
CRP3/MLP also interacts with the basic helix-loop-helix
myogenic transcription factors MyoD, myogenin, and MRF4
thereby increasing their affinity for specific DNA
regulatory elements. LIM domains are 50-60 amino acids
in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 54
Score = 30.1 bits (67), Expect = 0.12
Identities = 15/34 (44%), Positives = 21/34 (61%), Gaps = 1/34 (2%)
Query: 28 WHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
WH C RCA+C + L E+ T ++G+ YCK Y
Sbjct: 21 WHKNCFRCAKCGKSL-ESTTLTEKEGEIYCKGCY 53
>gnl|CDD|188785 cd09401, LIM_TLP_like, The LIM domains of thymus LIM protein
(TLP). The LIM domain of thymus LIM protein (TLP) like
proteins: This family includes the LIM domains of TLP
and CRIP (Cysteine-Rich Intestinal Protein). TLP is the
distant member of the CRP family of proteins. TLP has
two isomers (TLP-A and TLP-B) and sharing approximately
30% with each of the three other CRPs. Like CRP1, CRP2
and CRP3/MLP, TLP has two LIM domains, connected by a
flexible linker region. Unlike the CRPs, TLP lacks the
nuclear targeting signal (K/R-K/R-Y-G-P-K) and is
localized solely in the cytoplasm. TLP is specifically
expressed in the thymus in a subset of cortical
epithelial cells. TLP has a role in development of
normal thymus and in controlling the development and
differentiation of thymic epithelial cells. CRIP is a
short LIM protein with only one LIM domain. CRIP gene
is developmentally regulated and can be induced by
glucocorticoid hormones during the first three
postnatal weeks. The domain shows close sequence
homology to LIM domain of thymus LIM protein. However,
unlike the TLP proteins which have two LIM domains, the
members of this family have only one LIM domain. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 53
Score = 29.6 bits (67), Expect = 0.14
Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 27 EWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
+WH CLRC +C + L +GK YC + Y
Sbjct: 20 DWHKPCLRCEKCKKTLTPGQHS-EHEGKPYCNKCY 53
>gnl|CDD|188788 cd09404, LIM1_MLP84B_like, The LIM domain of Mlp84B and Mlp60A.
The LIM domain of Mlp84B and Mlp60A: Mlp84B and Mlp60A
belong to the CRP LIM domain protein family. The Mlp84B
protein contains five copies of the LIM domains, each
followed by a Glycin Rich Region (GRR). However, only
the first LIM domain of Mlp84B is in this family.
Mlp60A exhibits only one LIM domain linked to a
glycin-rich region. Mlp84B and Mlp60A are muscle
specific proteins and have been implicated in muscle
differentiation. While Mlp84B transcripts are enriched
at the terminal ends of muscle fibers, Mlp60A
transcripts are found throughout the muscle fibers. All
LIM domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 54
Score = 29.8 bits (67), Expect = 0.15
Identities = 14/38 (36%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 21 RVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCK 58
R+A +WH C +C C++ LD + C +G+ YCK
Sbjct: 15 RLAGGYKWHKMCFKCGMCNKLLD-STNCAEHEGELYCK 51
>gnl|CDD|188736 cd09350, LIM1_TRIP6, The first LIM domain of Thyroid
receptor-interacting protein 6 (TRIP6). The first LIM
domain of Thyroid receptor-interacting protein 6
(TRIP6): TRIP6 is a member of the zyxin LIM protein
family and contains three LIM zinc-binding domains at
the C-terminal. TRIP6 protein localizes to focal
adhesion sites and along actin stress fibers.
Recruitment of this protein to the plasma membrane
occurs in a lysophosphatidic acid (LPA)-dependent
manner. TRIP6 recruits a number of molecules involved in
actin assembly, cell motility, survival and
transcriptional control. The function of TRIP6 in cell
motility is regulated by Src-dependent phosphorylation
at a Tyr residue. The phosphorylation activates the
coupling to the Crk SH2 domain, which is required for
the function of TRIP6 in promoting lysophosphatidic acid
(LPA)-induced cell migration. TRIP6 can shuttle to the
nucleus to serve as a coactivator of AP-1 and NF-kappaB
transcriptional factors. Moreover, TRIP6 can form a
ternary complex with the NHERF2 PDZ protein and LPA2
receptor to regulate LPA-induced activation of ERK and
AKT, rendering cells resistant to chemotherapy. Recent
evidence shows that TRIP6 antagonizes Fas-Induced
apoptosis by enhancing the antiapoptotic effect of LPA
in cells. As in other LIM domains, this domain family is
50-60 amino acids in size and shares two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 54
Score = 29.3 bits (66), Expect = 0.17
Identities = 12/36 (33%), Positives = 19/36 (52%)
Query: 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQL 132
C +C N E A ++++HV CF C+ C +L
Sbjct: 1 CGRCGENVVGEGTGCTAMDQVFHVDCFTCMTCNGKL 36
>gnl|CDD|188866 cd09482, LIM2_CRP3, The second LIM domain of Cysteine Rich
Protein 3 (CRP3/MLP). The second LIM domain of
Cysteine Rich Protein 3 (CRP3/MLP): Cysteine-rich
proteins (CRPs) are characterized by the presence of
two LIM domains linked to short glycine-rich repeats
(GRRs). The CRP family members include CRP1, CRP2,
CRP3/MLP and TLPCRP1, CRP2 and CRP3 share a conserved
nuclear targeting signal (K/R-K/R-Y-G-P-K), which
supports the fact that these proteins function not only
in the cytoplasm but also in the nucleus. CRPs control
regulatory pathways during cellular differentiation,
and involve in complex transcription circuits, and the
organization as well as the arrangement of the
myofibrillar/cytoskeletal network.CRP3 also called
Muscle LIM Protein (MLP), which is a striated
muscle-specific factor that enhances myogenic
differentiation. The second LIM domain of CRP3/MLP
interacts with cytoskeletal protein beta-spectrin.
CRP3/MLP also interacts with the basic helix-loop-helix
myogenic transcription factors MyoD, myogenin, and MRF4
thereby increasing their affinity for specific DNA
regulatory elements. LIM domains are 50-60 amino acids
in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 54
Score = 29.2 bits (65), Expect = 0.21
Identities = 16/34 (47%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 28 WHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
WH C RCA C + L E+ T +DG+ YCK Y
Sbjct: 21 WHKTCFRCAICGKSL-ESTTVTDKDGELYCKVCY 53
>gnl|CDD|188749 cd09363, LIM3_Enigma_like, The third LIM domain of Enigma-like
family. The third LIM domain of Enigma-like family:
The Enigma LIM domain family is comprised of three
members: Enigma, ENH, and Cypher (mouse)/ZASP (human).
These subfamily members contain a single PDZ domain at
the N-terminus and three LIM domains at the C-terminus.
Enigma was initially characterized in humans and is
expressed in multiple tissues, such as skeletal muscle,
heart, bone, and brain. The third LIM domain
specifically interacts with the insulin receptor and
the second LIM domain interacts with the receptor
tyrosine kinase Ret and the adaptor protein APS. Thus
Enigma is implicated in signal transduction processes,
such as mitogenic activity, insulin related actin
organization, and glucose metabolism. The second
member, ENH protein, was first identified in rat brain.
It has been shown that ENH interacts with protein
kinase D1 (PKD1) via its LIM domains and forms a
complex with PKD1 and the alpha1C subunit of cardiac
L-type voltage-gated calcium channel in rat neonatal
cardiomyocytes. The N-terminal PDZ domain interacts
with alpha-actinin at the Z-line. ZASP/Cypher is
required for maintenance of Z-line structure during
muscle contraction, but not required for Z-line
assembly. In heart, Cypher/ZASP plays a structural role
through its interaction with cytoskeletal Z-line
proteins. In addition, there is increasing evidence
that Cypher/ZASP also performs signaling functions.
Studies reveal that Cypher/ZASP interacts with and
directs PKC to the Z-line, where PKC phosphorylates
downstream signaling targets. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 54
Score = 28.9 bits (65), Expect = 0.22
Identities = 18/52 (34%), Positives = 20/52 (38%), Gaps = 1/52 (1%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCK 58
C GC I A WH C CA CH L E T + + K CK
Sbjct: 1 CHGCDFPIEAGDRFLEALGHTWHDTCFVCAVCHVNL-EGQTFYSKKDKPLCK 51
Score = 27.8 bits (62), Expect = 0.59
Identities = 15/52 (28%), Positives = 22/52 (42%), Gaps = 1/52 (1%)
Query: 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCK 148
C C+ + D + A +H CF C VC + G F ++D CK
Sbjct: 1 CHGCDFPIEAGDRFLEALGHTWHDTCFVCAVC-HVNLEGQTFYSKKDKPLCK 51
>gnl|CDD|188797 cd09413, LIM1_Testin, The first LIM domain of Testin. The first
LIM domain of Testin: Testin contains three C-terminal
LIM domains and a PET protein-protein interaction
domain at the N-terminal. Testin is a cytoskeleton
associated focal adhesion protein that localizes along
actin stress fibers, at cell-cell-contact areas, and at
focal adhesion plaques. Testin interacts with a variety
of cytoskeletal proteins, including zyxin, mena, VASP,
talin, and actin and it is involved in cell motility
and adhesion events. Knockout mice experiments reveal
that tumor repressor function of Testin. LIM domains
are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 58
Score = 29.3 bits (66), Expect = 0.22
Identities = 17/44 (38%), Positives = 22/44 (50%), Gaps = 1/44 (2%)
Query: 18 YILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
Y R D WH AC C+ C + L + F ++GK YC R Y
Sbjct: 16 YAERAGYDKLWHPACFVCSTCGELL-VDMIYFWKNGKLYCGRHY 58
Score = 26.7 bits (59), Expect = 2.0
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 4/41 (9%)
Query: 97 CEKCNLNFKREDFVMRAK----NKIYHVQCFCCVVCGKQLV 133
C C K D + A+ +K++H CF C CG+ LV
Sbjct: 1 CYCCKQPMKEGDPAVYAERAGYDKLWHPACFVCSTCGELLV 41
>gnl|CDD|188784 cd09400, LIM_like_1, LIM domain in proteins of unknown function.
LIM domain in proteins of unknown function: LIM domains
are identified in a diverse group of proteins with wide
variety of biological functions, including gene
expression regulation, cell fate determination,
cytoskeleton organization, tumor formation, and
development. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes. They perform their functions through
interactions with other protein partners. The LIM
domains are 50-60 amino acids in size and share two
characteristic highly conserved zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. The consensus sequence of LIM domain
has been defined as
C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,
21)-C-x(2,3)-[CHD] (where X denotes any amino acid).
Length = 61
Score = 28.9 bits (65), Expect = 0.27
Identities = 18/52 (34%), Positives = 24/52 (46%), Gaps = 2/52 (3%)
Query: 96 KCEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFC 147
C C L + ++ K+YH CF C CG QL PG + E G +C
Sbjct: 4 PCASCGLPVFLAERLLIEG-KVYHRTCFKCARCGVQLTPGSFYET-EYGSYC 53
>gnl|CDD|188841 cd09457, LIM2_ENH, The second LIM domain of the Enigma Homolog
(ENH) family. The second LIM domain of the Enigma
Homolog (ENH) family: ENH was initially identified in
rat brain. Same as enigma, it contains three LIM
domains at the C-terminus and a PDZ domain at
N-terminus. ENH is implicated in signal transduction
processes involving protein kinases. It has also been
shown that ENH interacts with protein kinase D1 (PKD1)
via its LIM domains and forms a complex with PKD1 and
the alpha1C subunit of cardiac L-type voltage-gated
calcium channel in rat neonatal cardiomyocytes. The
N-terminal PDZ domain interacts with alpha-actinin at
the Z-line. ENH is expressed in multiple tissues, such
as skeletal muscle, heart, bone, and brain. LIM domains
are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 52
Score = 28.8 bits (64), Expect = 0.29
Identities = 13/34 (38%), Positives = 18/34 (52%), Gaps = 1/34 (2%)
Query: 28 WHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
WH +C C CH + N + DG+ YC+ DY
Sbjct: 20 WHVSCFVCVACHNPI-RNNVFHLEDGEPYCETDY 52
Score = 27.7 bits (61), Expect = 0.76
Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 3/55 (5%)
Query: 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKDDH 151
C +C E V+ A + +HV CF CV C + + F L + +C+ D+
Sbjct: 1 CGRCQRKILGE--VINALKQTWHVSCFVCVACHNP-IRNNVFHLEDGEPYCETDY 52
>gnl|CDD|188739 cd09353, LIM2_Zyxin, The second LIM domain of Zyxin. The second
LIM domain of Zyxin: Zyxin exhibits three copies of the
LIM domain, an extensive proline-rich domain and a
nuclear export signal. Localized at sites of
cellsubstratum adhesion in fibroblasts, Zyxin interacts
with alpha-actinin, members of the cysteine-rich protein
(CRP) family, proteins that display Src homology 3 (SH3)
domains and Ena/VASP family members. Zyxin and its
partners have been implicated in the spatial control of
actin filament assembly as well as in pathways important
for cell differentiation. In addition to its functions
at focal adhesion plaques, recent work has shown that
zyxin moves from the sites of cell contacts to the
nucleus, where it directly participates in the
regulation of gene expression. As in other LIM domains,
this domain family is 50-60 amino acids in size and
shares two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors o r
scaffolds to support the assembly of multimeric protein.
Length = 60
Score = 28.7 bits (64), Expect = 0.30
Identities = 12/21 (57%), Positives = 15/21 (71%)
Query: 108 DFVMRAKNKIYHVQCFCCVVC 128
D +++A K YH QCF CVVC
Sbjct: 10 DRMLKATGKSYHPQCFTCVVC 30
>gnl|CDD|188848 cd09464, LIM2_LIMK1, The second LIM domain of LIMK1 (LIM domain
Kinase 1). The second LIM domain of LIMK1 (LIM domain
Kinase 1): LIMK1 belongs to the LIMK protein family,
which comprises LIMK1 and LIMK2. LIMK contains two LIM
domains, a PDZ domain, and a kinase domain. LIMK is
involved in the regulation of actin polymerization and
microtubule disassembly. LIMK influences architecture of
the actin cytoskeleton by regulating the activity of the
cofilin family proteins cofilin1, cofilin2, and destrin.
The mechanism of the activation is to phosphorylates
cofilin on serine 3 and inactivates its actin-severing
activity, and altering the rate of actin
depolymerization. LIMKs can function in both cytoplasm
and nucleus. Both LIMK1 and LIMK2 can act in the nucleus
to suppress Rac/Cdc42-dependent cyclin D1 expression.
LIMK1 is expressed in all tissues and is localized to
focal adhesions in the cell. LIMK1 can form homodimers
upon binding of HSP90 and is activated by Rho effector
Rho kinase and MAPKAPK2. LIMK1 is important for normal
central nervous system development, and its deletion has
been implicated in the development of the human genetic
disorder Williams syndrome. Moreover, LIMK1 up-regulates
the promoter activity of urokinase type plasminogen
activator and induces its mRNA and protein expression in
breast cancer cells. The LIM domains have been shown to
play an important role in regulating kinase activity and
likely also contribute to LIMK function by acting as
sites of protein-to-protein interactions. All LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 55
Score = 28.7 bits (64), Expect = 0.32
Identities = 17/40 (42%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 109 FVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDG-LFC 147
VM A + YH +CF C+ CG + GD +AL E L+C
Sbjct: 12 LVMVAGEQKYHPECFSCLRCGAFIGDGDTYALVEHSKLYC 51
>gnl|CDD|188741 cd09355, LIM2_Ajuba_like, The second LIM domain of Ajuba-like
proteins. The second LIM domain of Ajuba-like
proteins: Ajuba like LIM protein family includes three
highly homologous proteins Ajuba, Limd1, and WTIP.
Members of the family contain three tandem C-terminal
LIM domains and a proline-rich N-terminal region. This
family of proteins functions as scaffolds,
participating in the assembly of numerous protein
complexes. In the cytoplasm, Ajuba binds Grb2 to
modulate serum-stimulated ERK activation. Ajuba also
recruits the TNF receptor-associated factor 6 (TRAF6)
to p62 and activates PKCKappa activity. Ajuba interacts
with alpha-catenin and F-actin to contribute to the
formation or stabilization of adheren junctions by
linking adhesive receptors to the actin cytoskeleton.
Although Ajuba is a cytoplasmic protein, it can shuttle
into the nucleus. In nucleus, Ajuba functions as a
corepressor for the zinc finger-protein Snail. It binds
to the SNAG repression domain of Snail through its LIM
region. Arginine methyltransferase-5 (Prmt5), a
protein in the complex, is recruited to Snai l through
an interaction with Ajuba. This ternary complex
functions to repress E-cadherin, a Snail target gene.
In addition, Ajuba contains functional nuclear-receptor
interacting motifs and selectively interacts with
retinoic acid receptors (RARs) and rexinoid receptor
(RXRs) to negatively regulate retinoic acid signaling.
Wtip, the Wt1-interacting protein, was originally
identified as an interaction partner of the Wilms
tumour protein 1 (WT1). Wtip is involved in kidney and
neural crest development. Wtip interacts with the
receptor tyrosine kinase Ror2 and inhibits canonical
Wnt signaling. LIMD1 was reported to inhibit cell
growth and metastases. The inhibition may be mediated
through an interaction with the protein
barrier-to-autointegration (BAF), a component of
SWI/SNF chromatin-remodeling protein; or through the
interaction with retinoblastoma protein (pRB),
resulting in inhibition of E2F-mediated transcription,
and expression of the majority of genes with E2F1-
responsive elements. Recently, Limd1 was shown to
interact with the p62/sequestosome protein and
influence IL-1 and RANKL signaling by facilitating the
assembly of a p62/TRAF6/a-PKC multi-protein complex.
The Limd1-p62 interaction affects both NF-kappaB and
AP-1 activity in epithelial cells and osteoclasts.
Moreover, LIMD1 functions as tumor repressor to block
lung tumor cell line in vitro and in vivo. Recent
studies revealed that LIM proteins Wtip, LIMD1 and
Ajuba interact with components of RNA induced silencing
complexes (RISC) as well as eIF4E and the mRNA m7GTP
cap-protein complex and are required for
microRNA-mediated gene silencing. As in other LIM
domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein.
Length = 53
Score = 28.5 bits (64), Expect = 0.35
Identities = 15/55 (27%), Positives = 23/55 (41%), Gaps = 2/55 (3%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
C CG I + + + +H C RC C++ LD + YC +DY
Sbjct: 1 CAVCGHLIMEMILQALGKS--YHPGCFRCCVCNECLDGVPFTVDVENNIYCVKDY 53
Score = 24.6 bits (54), Expect = 9.4
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 108 DFVMRAKNKIYHVQCFCCVVCGKQL 132
+ +++A K YH CF C VC + L
Sbjct: 10 EMILQALGKSYHPGCFRCCVCNECL 34
>gnl|CDD|188820 cd09436, LIM3_TRIP6, The third LIM domain of Thyroid
receptor-interacting protein 6 (TRIP6). The third LIM
domain of Thyroid receptor-interacting protein 6
(TRIP6): TRIP6 is a member of the zyxin LIM protein
family and contains three LIM zinc-binding domains at
the C-terminal. TRIP6 protein localizes to focal
adhesion sites and along actin stress fibers.
Recruitment of this protein to the plasma membrane
occurs in a lysophosphatidic acid (LPA)-dependent
manner. TRIP6 recruits a number of molecules involved
in actin assembly, cell motility, survival and
transcriptional control. The function of TRIP6 in cell
motility is regulated by Src-dependent phosphorylation
at a Tyr residue. The phosphorylation activates the
coupling to the Crk SH2 domain, which is required for
the function of TRIP6 in promoting lysophosphatidic
acid (LPA)-induced cell migration. TRIP6 can shuttle to
the nucleus to serve as a coactivator of AP-1 and
NF-kappaB transcriptional factors. Moreover, TRIP6 can
form a ternary complex with the NHERF2 PDZ protein and
LPA2 receptor to regulate LPA-induced activation of ERK
and AKT, rendering cells resistant to chemotherapy.
Recent evidence shows that TRIP6 antagonizes
Fas-Induced apoptosis by enhancing the antiapoptotic
effect of LPA in cells. As in other LIM domains, this
domain family is 50-60 amino acids in size and shares
two characteristic zinc finger motifs. The two zinc
fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to
two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric
protein.
Length = 66
Score = 28.8 bits (64), Expect = 0.37
Identities = 16/39 (41%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 22 VAPDLEWHAACLRCAECHQFLDE--NCTCFVRDGKTYCK 58
VA D ++H C RC +C L E N C+ DG CK
Sbjct: 21 VALDRDFHVQCYRCEDCGSLLSEGDNQGCYPLDGHILCK 59
>gnl|CDD|188805 cd09421, LIM3_LIMPETin, The third LIM domain of protein LIMPETin.
The third LIM domain of protein LIMPETin: LIMPETin
contains 6 LIM domains at the C-terminal and an
N-terminal PET domain. Four of the six LIM domains are
highly homologous to the four and half LIM domain
protein family and two of them show sequence similarity
to the LIM domains of the testin family. Thus, LIMPETin
may be the recombinant product of genes coding testin
and FHL proteins. In Schistosoma mansoni, where
LIMPETin was first identified, LIMPETin is down
regulated in sexually mature adult Schistosoma females
compared to sexually immature adult females and adult
male. Its differential expression indicates that it is a
transcription regulator. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 59
Score = 28.7 bits (64), Expect = 0.39
Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 1/55 (1%)
Query: 93 FGTKCEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFC 147
F +CE+C+ + + K+K +H CF C C LV F + D ++C
Sbjct: 1 FANQCEECSKIIGIDSKDLSYKDKHWHEACFLCSKCKISLV-DKPFGSKADRIYC 54
>gnl|CDD|188782 cd09396, LIM_DA1, The Lim domain of DA1. The Lim domain of DA1:
DA1 contains one copy of LIM domain and a domain of
unknown function. DA1 is predicted as an ubiquitin
receptor, which sets final seed and organ size by
restricting the period of cell proliferation. The LIM
domain is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein.
Length = 53
Score = 28.4 bits (64), Expect = 0.41
Identities = 13/53 (24%), Positives = 22/53 (41%), Gaps = 2/53 (3%)
Query: 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKD 149
C C F+ A ++H +CF C C K + EF++ + + K
Sbjct: 1 CAGCKSEIGHGRFL-SALGAVWHPECFRCHACRKPI-AEHEFSVSGNDPYHKS 51
>gnl|CDD|188829 cd09445, LIM_Mical_like_2, This domain belongs to the LIM domain
family which are found on Mical (molecule interacting
with CasL) like proteins. The LIM domain on proteins of
unknown function: This domain belongs to the LIM domain
family which are found on Mical (molecule interacting
with CasL)-like proteins. Known members of the
Mical-like family includes single LIM domain containing
proteins, Mical (molecule interacting with CasL), pollen
specific protein SF3, Eplin, xin actin-binding
repeat-containing protein 2 (XIRP2), and Ltd-1. The
members of this family function mainly at the
cytoskeleton and focal adhesions. They interact with
transcription factors or other signaling molecules to
play roles in muscle development, neuronal
differentiation, cell growth, and mobility. As in other
LIM domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 53
Score = 28.2 bits (63), Expect = 0.43
Identities = 16/36 (44%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 113 AKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCK 148
A+ IYH CF C C KQL D + E L+CK
Sbjct: 16 AEKHIYHKNCFRCKDCNKQLKV-DNYQSHEGNLYCK 50
>gnl|CDD|188751 cd09365, LIM2_LIMK, The second LIM domain of LIMK (LIM domain
Kinase ). The second LIM domain of LIMK (LIM domain
Kinase ): LIMK protein family is comprised of two
members LIMK1 and LIMK2. LIMK contains two LIM domains,
a PDZ domain and a kinase domain. LIMK is involved in
the regulation of actin polymerization and microtubule
disassembly. LIMK influences architecture of the actin
cytoskeleton by regulating the activity of the cofilin
family proteins cofilin1, cofilin2, and destrin. The
mechanism of the activation is to phosphorylates cofilin
on serine 3 and inactivates its actin-severing activity,
and altering the rate of actin depolymerization. LIMKs
can function in both cytoplasm and nucleus and are
expressed in all tissues. Both LIMK1 and LIMK2 can act
in the nucleus to suppress Rac/Cdc42-dependent cyclin D1
expression. However, LIMK1 and LIMk2 have different
cellular locations. While LIMK1 localizes mainly at
focal adhesions, LIMK2 is found in cytoplasmic punctae,
suggesting that they may have different cellular
functions. The LIM domains of LIMK have been shown to
play an important role in regulating kinase activity and
likely also contribute to LIMK function by acting as
sites of protein-to-protein interactions. All LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 54
Score = 28.1 bits (63), Expect = 0.45
Identities = 13/33 (39%), Positives = 18/33 (54%)
Query: 110 VMRAKNKIYHVQCFCCVVCGKQLVPGDEFALRE 142
VM A + +H +CF C C + GD +AL E
Sbjct: 12 VMVAGDHKFHPECFSCSSCKAFIGDGDSYALVE 44
>gnl|CDD|188738 cd09352, LIM1_Ajuba_like, The first LIM domain of Ajuba-like
proteins. The first LIM domain of Ajuba-like proteins:
Ajuba like LIM protein family includes three highly
homologous proteins Ajuba, Limd1, and WTIP. Members of
the family contain three tandem C-terminal LIM domains
and a proline-rich N-terminal region. This family of
proteins functions as scaffolds, participating in the
assembly of numerous protein complexes. In the
cytoplasm, Ajuba binds Grb2 to modulate serum-stimulated
ERK activation. Ajuba also recruits the TNF
receptor-associated factor 6 (TRAF6) to p62 and
activates PKCKappa activity. Ajuba interacts with
alpha-catenin and F-actin to contribute to the formation
or stabilization of adheren junctions by linking
adhesive receptors to the actin cytoskeleton. Although
Ajuba is a cytoplasmic protein, it can shuttle into the
nucleus. In nucleus, Ajuba functions as a corepressor
for the zinc finger-protein Snail. It binds to the SNAG
repression domain of Snail through its LIM region.
Arginine methyltransferase-5 (Prmt5), a protein in the
complex, is recruited to Snai l through an interaction
with Ajuba. This ternary complex functions to repress
E-cadherin, a Snail target gene. In addition, Ajuba
contains functional nuclear-receptor interacting motifs
and selectively interacts with retinoic acid receptors
(RARs) and rexinoid receptor (RXRs) to negatively
regulate retinoic acid signaling. Wtip, the
Wt1-interacting protein, was originally identified as an
interaction partner of the Wilms tumour protein 1 (WT1).
Wtip is involved in kidney and neural crest development.
Wtip interacts with the receptor tyrosine kinase Ror2
and inhibits canonical Wnt signaling. LIMD1 was reported
to inhibit cell growth and metastases. The inhibition
may be mediated through an interaction with the protein
barrier-to-autointegration (BAF), a component of SWI/SNF
chromatin-remodeling protein; or through the interaction
with retinoblastoma protein (pRB), resulting in
inhibition of E2F-mediated transcription, and expression
of the majority of genes with E2F1- responsive elements.
Recently, Limd1 was shown to interact with the
p62/sequestosome protein and influence IL-1 and RANKL
signaling by facilitating the assembly of a
p62/TRAF6/a-PKC multi-protein complex. The Limd1-p62
interaction affects both NF-kappaB and AP-1 activity in
epithelial cells and osteoclasts. Moreover, LIMD1
functions as tumor repressor to block lung tumor cell
line in vitro and in vivo. Recent studies revealed that
LIM proteins Wtip, LIMD1 and Ajuba interact with
components of RNA induced silencing complexes (RISC) as
well as eIF4E and the mRNA m7GTP cap-protein complex and
are required for microRNA-mediated gene silencing. As
in other LIM domains, this domain family is 50-60 amino
acids in size and shares two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 54
Score = 28.2 bits (63), Expect = 0.48
Identities = 16/54 (29%), Positives = 23/54 (42%), Gaps = 1/54 (1%)
Query: 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKDD 150
C KC +A +YH CF C CG+ L G F ++C++D
Sbjct: 1 CVKCGKGVYGASQACQAMGNLYHTNCFTCCSCGRTL-RGKAFYNVNGKVYCEED 53
>gnl|CDD|188849 cd09465, LIM2_LIMK2, The second LIM domain of LIMK2 (LIM domain
Kinase 2). The second LIM domain of LIMK2 (LIM domain
Kinase 2): LIMK2 is a member of the LIMK protein family,
which comprises LIMK1 and LIMK2. LIMK contains two LIM
domains, a PDZ domain, and a kinase domain. LIMK is
involved in the regulation of actin polymerization and
microtubule disassembly. LIMK influences architecture of
the actin cytoskeleton by regulating the activity of the
cofilin family proteins cofilin1, cofilin2, and destrin.
The mechanism of the activation is to phosphorylates
cofilin on serine 3 and inactivates its actin-severing
activity, altering the rate of actin depolymerisation.
LIMK activity is activated by phosphorylation of a
threonine residue within the activation loop of the
kinase by p21-activated kinases 1 and 4 and by Rho
kinase. LIMKs can function in both cytoplasm and
nucleus. Both LIMK1 and LIMK2 can act in the nucleus to
suppress Rac/Cdc42-dependent cyclin D1 expression. LIMK2
is expressed in all tissues. While LIMK1 localizes
mainly at focal adhesions, LIMK2 is found in cytoplasmic
punctae, suggesting that they may have different
cellular functions. The activity of LIM kinase 2 to
regulate cofilin phosphorylation is inhibited by the
direct binding of Par-3. LIMK2 activation promotes cell
cycle progression. The phenotype of Limk2 knockout mice
shows a defect in spermatogenesis. The LIM domains have
been shown to play an important role in regulating
kinase activity and likely also contribute to LIMK
function by acting as sites of protein-to-protein
interactions. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 59
Score = 28.4 bits (63), Expect = 0.53
Identities = 20/60 (33%), Positives = 27/60 (45%), Gaps = 3/60 (5%)
Query: 93 FGTKCEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDG-LFCKDDH 151
FG C C+L M A YH +CF C+ C + GD +AL + L+C H
Sbjct: 2 FGELCHGCSLLMTGP--AMVAGEYKYHPECFACMSCKVIIEDGDTYALVQHTTLYCGKCH 59
>gnl|CDD|188729 cd09343, LIM1_FHL, The first LIM domain of Four and a half LIM
domains protein (FHL). The first LIM domain of Four and
a half LIM domains protein (FHL): LIM-only protein
family consists of five members, designated FHL1, FHL2,
FHL3, FHL5 and LIMPETin. The first four members are
composed of four complete LIM domains arranged in tandem
and an N-terminal single zinc finger domain with a
consensus sequence equivalent to the C-terminal half of
a LIM domain. LIMPETin is an exception, containing six
LIM domains. FHL1, 2 and 3 are predominantly expressed
in muscle tissues, and FHL5 is highly expressed in male
germ cells. FHL proteins exert their roles as
transcription co-activators or co-repressors through a
wide array of interaction partners. For example, FHL1
binds to Myosin-binding protein C, regulating myosin
filament formation and sarcomere assembly. FHL2 has
shown to interact with more than 50 different proteins,
including receptors, structural proteins, transcription
factors and cofactors, signal transducers, splicing
factors, DNA replication and repair enzymes, and
metabolic enzymes. FHL3 int eracts with many
transcription factors, such as CREB, BKLF/KLF3, CtBP2,
MyoD, and MZF_1. FHL5 is a tissue-specific coactivator
of CREB/CREM family transcription factors. LIM domains
are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 59
Score = 28.2 bits (63), Expect = 0.55
Identities = 16/57 (28%), Positives = 27/57 (47%), Gaps = 1/57 (1%)
Query: 93 FGTKCEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKD 149
F CE+C + + K++ +H CF C C + LV FA +++ L C +
Sbjct: 1 FANTCEECKKKIGCDSKDLSYKDRHWHEGCFKCFKCQRSLVD-KPFAAKDEDLLCTE 56
>gnl|CDD|240339 PTZ00265, PTZ00265, multidrug resistance protein (mdr1);
Provisional.
Length = 1466
Score = 30.4 bits (68), Expect = 0.64
Identities = 16/34 (47%), Positives = 22/34 (64%), Gaps = 3/34 (8%)
Query: 148 KDDHEGMDKSSNGENNNNNTNINNNLHNLNNEGS 181
KD+ E +K++ +NNNNN N NN +NN GS
Sbjct: 672 KDNKENNNKNNKDDNNNNNNNNNN---KINNAGS 702
>gnl|CDD|188794 cd09410, LIM3_Leupaxin, The third LIM domain of Leupaxin. The
third LIM domain of Leupaxin: Leupaxin is a
cytoskeleton adaptor protein, which is preferentially
expressed in hematopoietic cells. Leupaxin belongs to
the paxillin focal adhesion protein family. Same as
other members of the family, it has four leucine-rich
LD-motifs in the N-terminus and four LIM domains in the
C-terminus. It may function in cell type-specific
signaling by associating with interaction partners
PYK2, FAK, PEP and p95PKL. When expressed in human
leukocytic cells, leupaxin significantly suppressed
integrin-mediated cell adhesion to fibronectin and the
tyrosine phosphorylation of paxillin. These findings
indicate that leupaxin may negatively regulate the
functions of paxillin during integrin signaling. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 53
Score = 27.9 bits (62), Expect = 0.67
Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 3/55 (5%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
C GCG + + Y+ A + WH C C++C + + F DG+ C+ Y
Sbjct: 1 CSGCGRPVKENYL--SAANGVWHPECFVCSDCLKPFTDGSF-FELDGRPLCELHY 52
>gnl|CDD|188813 cd09429, LIM3_FHL1, The third LIM domain of Four and a half LIM
domains protein 1 (FHL1). The third LIM domain of Four
and a half LIM domains protein 1 (FHL1): FHL1 is
heavily expressed in skeletal and cardiac muscles. It
plays important roles in muscle growth, differentiation,
and sarcomere assembly by acting as a modulator of
transcription factors. Defects in FHL1 gene are
responsible for a number of Muscular dystrophy-like
muscle disorders. It has been detected that FHL1 binds
to Myosin-binding protein C, regulating myosin filament
formation and sarcomere assembly. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 53
Score = 27.5 bits (61), Expect = 0.73
Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 118 YHVQCFCCVVCGKQLVPGDEFALREDGLFCKD 149
+H +CF C C K+L G F ED +C D
Sbjct: 20 WHSECFVCSSCSKKLA-GQRFTAVEDQYYCVD 50
>gnl|CDD|188732 cd09346, LIM3_FHL, The third LIM domain of Four and a half LIM
domains protein (FHL). The third LIM domain of Four and
a half LIM domains protein (FHL): LIM-only protein
family consists of five members, designated FHL1, FHL2,
FHL3, FHL5 and LIMPETin. The first four members are
composed of four complete LIM domains arranged in tandem
and an N-terminal single zinc finger domain with a
consensus sequence equivalent to the C-terminal half of
a LIM domain. LIMPETin is an exception, containing six
LIM domains. FHL1, 2 and 3 are predominantly expressed
in muscle tissues, and FHL5 is highly expressed in male
germ cells. FHL proteins exert their roles as
transcription co-activators or co-repressors through a
wide array of interaction partners. For example, FHL1
binds to Myosin-binding protein C, regulating myosin
filament formation and sarcomere assembly. FHL2 has
shown to interact with more than 50 different proteins,
including receptors, structural proteins, transcription
factors and cofactors, signal transducers, splicing
factors, DNA replication and repair enzymes, and
metabolic enzymes. FHL3 int eracts with many
transcription factors, such as CREB, BKLF/KLF3, CtBP2,
MyoD, and MZF_1. FHL5 is a tissue-specific coactivator
of CREB/CREM family transcription factors. LIM domains
are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 52
Score = 27.7 bits (62), Expect = 0.76
Identities = 13/36 (36%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 114 KNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKD 149
+++ +H +CF C C KQL G F R++ +C D
Sbjct: 16 RDQPWHKECFVCTGCKKQLA-GQRFTSRDEYPYCVD 50
>gnl|CDD|188843 cd09459, LIM3_ENH, The third LIM domain of the Enigma Homolog (ENH)
family. The third LIM domain of the Enigma Homolog
(ENH) family: ENH was initially identified in rat brain.
Same as enigma, it contains three LIM domains at the
C-terminus and a PDZ domain at N-terminus. ENH is
implicated in signal transduction processes involving
protein kinases. It has also been shown that ENH
interacts with protein kinase D1 (PKD1) via its LIM
domains and forms a complex with PKD1 and the alpha1C
subunit of cardiac L-type voltage-gated calcium channel
in rat neonatal cardiomyocytes. The N-terminal PDZ
domain interacts with alpha-actinin at the Z-line. ENH
is expressed in multiple tissues, such as skeletal
muscle, heart, bone, and brain. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 55
Score = 27.6 bits (61), Expect = 0.79
Identities = 16/52 (30%), Positives = 22/52 (42%), Gaps = 1/52 (1%)
Query: 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCK 148
C C + D + A +H CF C VC + L G F ++D CK
Sbjct: 1 CHGCEFPIEAGDRFLEALGHTWHDTCFVCSVCCESL-EGQTFFSKKDKPLCK 51
>gnl|CDD|188814 cd09430, LIM5_LIMPETin, The fifth LIM domain of protein LIMPETin.
The fifth LIM domain of protein LIMPETin: LIMPETin
contains 6 LIM domains at the C-terminal and an
N-terminal PET domain. Four of the six LIM domains are
highly homologous to the four and half LIM domain
protein family and two of them show sequence similarity
to the LIM domains of the testin family. Thus, LIMPETin
may be the recombinant product of genes coding testin
and FHL proteins. In Schistosoma mansoni, where
LIMPETin was first identified, LIMPETin is down
regulated in sexually mature adult Schistosoma females
compared to sexually immature adult females and adult
male. Its differential expression indicates that it is a
transcription regulator. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 52
Score = 27.4 bits (61), Expect = 0.94
Identities = 14/36 (38%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 114 KNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKD 149
KN+ +H +CF C C K L G F R++ +C D
Sbjct: 16 KNEPWHRECFTCTNCSKSLA-GQRFTSRDEKPYCAD 50
>gnl|CDD|188835 cd09451, LIM_RIL, The LIM domain of RIL. The LIM domain of RIL:
RIL contains an N-terminal PDZ domain, a LIM domain, and
a short consensus C-terminal region. It is the smallest
molecule in the ALP LIM domain containing protein
family. RIL was identified in rat fibroblasts and in
human lymphocytes. The LIM domain interacts with the
AMPA glutamate receptor in dendritic spines. The
consensus C-terminus interacts with PTP-BL, a
submembranous protein tyrosine phosphatase and the PDZ
domain is responsible to interact with alpha-actinin
molecules. LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 53
Score = 27.2 bits (60), Expect = 0.98
Identities = 13/39 (33%), Positives = 25/39 (64%), Gaps = 1/39 (2%)
Query: 110 VMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCK 148
+++A++K+YH +CF C CG L F + ++ L+C+
Sbjct: 12 IVKARDKLYHPECFMCDDCGLNLKQRGYFFI-DEQLYCE 49
>gnl|CDD|226305 COG3782, COG3782, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 289
Score = 29.5 bits (66), Expect = 1.0
Identities = 15/45 (33%), Positives = 20/45 (44%), Gaps = 1/45 (2%)
Query: 108 DFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALR-EDGLFCKDDH 151
DF+ R K +H++ C G Q P D + ED L K H
Sbjct: 113 DFLARLNGKPHHIELACKYYLGHQGGPEDWYGPDPEDRLLGKLAH 157
>gnl|CDD|188828 cd09444, LIM_Mical_like_1, This domain belongs to the LIM domain
family which are found on Mical (molecule interacting
with CasL) like proteins. The LIM domain on proteins of
unknown function: This domain belongs to the LIM domain
family which are found on Mical (molecule interacting
with CasL) like proteins. Known members of the
Mical-like family includes single LIM domain containing
proteins, Mical (molecule interacting with CasL), pollen
specific protein SF3, Eplin, xin actin-binding
repeat-containing protein 2 (XIRP2), and Ltd-1. The
members of this family function mainly at the
cytoskeleton and focal adhesions. They interact with
transcription factors or other signaling molecules to
play roles in muscle development, neuronal
differentiation, cell growth, and mobility. As in other
LIM domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 55
Score = 27.4 bits (61), Expect = 1.1
Identities = 14/34 (41%), Positives = 16/34 (47%)
Query: 113 AKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLF 146
K+YH CF C C L+PG A E G F
Sbjct: 16 VDGKLYHRNCFRCKECSSTLLPGSYKAGPEPGTF 49
>gnl|CDD|188792 cd09408, LIM2_Leupaxin, The second LIM domain of Leupaxin. The
second LIM domain of Leupaxin: Leupaxin is a
cytoskeleton adaptor protein, which is preferentially
expressed in hematopoietic cells. Leupaxin belongs to
the paxillin focal adhesion protein family. Same as
other members of the family, it has four leucine-rich
LD-motifs in the N-terminus and four LIM domains in the
C-terminus. It may function in cell type-specific
signaling by associating with interaction partners
PYK2, FAK, PEP and p95PKL. When expressed in human
leukocytic cells, leupaxin significantly suppressed
integrin-mediated cell adhesion to fibronectin and the
tyrosine phosphorylation of paxillin. These findings
indicate that leupaxin may negatively regulate the
functions of paxillin during integrin signaling. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 52
Score = 27.1 bits (60), Expect = 1.1
Identities = 21/56 (37%), Positives = 26/56 (46%), Gaps = 5/56 (8%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQ-FLDENCTCFVRDGKTYCKRDY 61
C C G I + A D WH C+ C + F DE RDGK YC+RD+
Sbjct: 1 CAYCAGPILQNVL--TAMDQTWHPEHFFCSHCGELFGDEGF--LERDGKPYCRRDF 52
>gnl|CDD|187889 cd09759, Cas6_I-A, CRISPR/Cas system-associated RAMP superfamily
protein Cas6. CRISPR (Clustered Regularly Interspaced
Short Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Cas6 is an endoribonuclease that generates crRNAs,
predicted subunit of Cascade complex; RAMP superfamily
protein; Possesses double RRM/ferredoxin fold.
Length = 240
Score = 28.9 bits (65), Expect = 1.3
Identities = 15/36 (41%), Positives = 18/36 (50%), Gaps = 7/36 (19%)
Query: 89 YVRLFGTKCEKCN-----LNFKREDFVMRAKNKIYH 119
YV +G+K EK N LNFK + R K YH
Sbjct: 170 YVEFYGSKPEKSNFEMEVLNFKPKRI--RIKPDTYH 203
>gnl|CDD|188845 cd09461, LIM3_Enigma_like_1, The third LIM domain of an Enigma
subfamily with unknown function. The third LIM domain
of an Enigma subfamily with unknown function: The
Enigma LIM domain family is comprised of three
characterized members: Enigma, ENH, and Cypher
(mouse)/ZASP (human). These subfamily members contain a
single PDZ domain at the N-terminus and three LIM
domains at the C-terminus. They serve as adaptor
proteins, where the PDZ domain tethers the protein to
the cytoskeleton and the LIM domains, recruit signaling
proteins to implement corresponding functions. The
members of the enigma family have been implicated in
regulating or organizing cytoskeletal structure, as
well as involving multiple signaling pathways. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 54
Score = 26.7 bits (59), Expect = 1.4
Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 1/52 (1%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCK 58
CV CG I A + +H+ C C C+ L E + + + G+ +CK
Sbjct: 1 CVSCGFPIEAGDRWVEALNNNYHSQCFNCTRCNVNL-EGQSFYAKGGRPFCK 51
Score = 26.0 bits (57), Expect = 3.2
Identities = 18/52 (34%), Positives = 21/52 (40%), Gaps = 1/52 (1%)
Query: 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCK 148
C C + D + A N YH QCF C C L G F + FCK
Sbjct: 1 CVSCGFPIEAGDRWVEALNNNYHSQCFNCTRCNVNL-EGQSFYAKGGRPFCK 51
>gnl|CDD|219500 pfam07655, Secretin_N_2, Secretin N-terminal domain. This is a
short domain found in bacterial type II/III secretory
system proteins. The architecture of these proteins
suggest that this family may be functionally analogous
to pfam03958.
Length = 95
Score = 27.7 bits (62), Expect = 1.5
Identities = 6/28 (21%), Positives = 18/28 (64%)
Query: 157 SSNGENNNNNTNINNNLHNLNNEGSNSG 184
S + +N++++ +N+ + ++ S+SG
Sbjct: 25 SVSSSGSNSSSSSSNSSNGGSSSSSSSG 52
>gnl|CDD|188806 cd09422, LIM1_FHL2, The first LIM domain of Four and a half LIM
domains protein 2 (FHL2). The first LIM domain of Four
and a half LIM domains protein 2 (FHL2): FHL2 is one of
the best studied FHL proteins. FHL2 expression is most
abundant in the heart, and in brain, liver and lung at
lesser extent. FHL2 participates in a wide range of
cellular processes, such as transcriptional regulation,
signal transduction, and cell survival by binding to
various protein partners. FHL2 has shown to interact
with more than 50 different proteins, including
receptors, structural proteins, transcription factors
and cofactors, signal transducers, splicing factors, DNA
replication and repair enzymes, and metabolic enzymes.
Although FHL2 is abundantly expressed in heart, the fhl2
null mice are viable and had no detectable abnormal
cardiac phenotype. LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 62
Score = 26.8 bits (59), Expect = 1.5
Identities = 16/57 (28%), Positives = 26/57 (45%), Gaps = 1/57 (1%)
Query: 93 FGTKCEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKD 149
+ CE+C + + K++ +H CF C C LV FA +E+ L C +
Sbjct: 1 YSNTCEECKKPIGCDCKDLSYKDRHWHESCFHCFQCKNSLV-DKPFAAKEEHLLCTE 56
>gnl|CDD|188827 cd09443, LIM_Ltd-1, The LIM domain of LIM and transglutaminase
domains protein (Ltd-1). The LIM domain of LIM and
transglutaminase domains protein (Ltd-1): This family
includes mouse Ky protein and Caenorhabditis elegans
Ltd-1 protein. The members of this family consists a
N-terminal Lim domain and a C-terminal
transglutaminase domain. The mouse Ky protein has
putative function in muscle development. The mouse with
ky mutant exhibits combined posterior and lateral
curvature of the spine. The Ltd-1 gene in C. elegans is
expressed in developing hypodermal cells from the
twofold stage embryo through adulthood. These data
define the ltd-1 gene as a novel marker for C. elegans
epithelial cell development. As in other LIM domains,
this domain family is 50-60 amino acids in size and
shares two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to
two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric
protein.
Length = 55
Score = 26.6 bits (59), Expect = 1.6
Identities = 13/34 (38%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 28 WHAACLRCAECHQFLDENCTCFVR-DGKTYCKRD 60
+H C +C EC L FV+ DG+ YC R
Sbjct: 21 YHKGCFKCRECGTRLSLKTFTFVQGDGEVYCARH 54
>gnl|CDD|188822 cd09438, LIM3_Ajuba_like, The third LIM domain of Ajuba-like
proteins. The third LIM domain of Ajuba-like proteins:
Ajuba like LIM protein family includes three highly
homologous proteins Ajuba, Limd1, and WTIP. Members of
the family contain three tandem C-terminal LIM domains
and a proline-rich N-terminal region. This family of
proteins functions as scaffolds, participating in the
assembly of numerous protein complexes. In the
cytoplasm, Ajuba binds Grb2 to modulate serum-stimulated
ERK activation. Ajuba also recruits the TNF
receptor-associated factor 6 (TRAF6) to p62 and
activates PKCKappa activity. Ajuba interacts with
alpha-catenin and F-actin to contribute to the formation
or stabilization of adheren junctions by linking
adhesive receptors to the actin cytoskeleton. Although
Ajuba is a cytoplasmic protein, it can shuttle into the
nucleus. In nucleus, Ajuba functions as a corepressor
for the zinc finger-protein Snail. It binds to the SNAG
repression domain of Snail through its LIM region.
Arginine methyltransferase-5 (Prmt5), a protein in the
complex, is recruited to Snai l through an interaction
with Ajuba. This ternary complex functions to repress
E-cadherin, a Snail target gene. In addition, Ajuba
contains functional nuclear-receptor interacting motifs
and selectively interacts with retinoic acid receptors
(RARs) and rexinoid receptor (RXRs) to negatively
regulate retinoic acid signaling. Wtip, the
Wt1-interacting protein, was originally identified as an
interaction partner of the Wilms tumour protein 1 (WT1).
Wtip is involved in kidney and neural crest development.
Wtip interacts with the receptor tyrosine kinase Ror2
and inhibits canonical Wnt signaling. LIMD1 was reported
to inhibit cell growth and metastases. The inhibition
may be mediated through an interaction with the protein
barrier-to-autointegration (BAF), a component of SWI/SNF
chromatin-remodeling protein; or through the interaction
with retinoblastoma protein (pRB), resulting in
inhibition of E2F-mediated transcription, and expression
of the majority of genes with E2F1- responsive elements.
Recently, Limd1 was shown to interact with the
p62/sequestosome protein and influence IL-1 and RANKL
signaling by facilitating the assembly of a
p62/TRAF6/a-PKC multi-protein complex. The Limd1-p62
interaction affects both NF-kappaB and AP-1 activity in
epithelial cells and osteoclasts. Moreover, LIMD1
functions as tumor repressor to block lung tumor cell
line in vitro and in vivo. Recent studies revealed that
LIM proteins Wtip, LIMD1 and Ajuba interact with
components of RNA induced silencing complexes (RISC) as
well as eIF4E and the mRNA m7GTP cap-protein complex and
are required for microRNA-mediated gene silencing. As
in other LIM domains, this domain family is 50-60 amino
acids in size and shares two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 62
Score = 26.6 bits (59), Expect = 2.0
Identities = 14/39 (35%), Positives = 18/39 (46%), Gaps = 2/39 (5%)
Query: 115 NKIYHVQCFCCVVCGKQLV--PGDEFALREDGLFCKDDH 151
+K YHV+C+ C CG QL G + L C H
Sbjct: 24 DKDYHVECYHCEDCGLQLNDEEGHRCYPLDGHLLCHSCH 62
>gnl|CDD|188789 cd09405, LIM1_Paxillin, The first LIM domain of paxillin. The
first LIM domain of paxillin: Paxillin is an adaptor
protein, which recruits key components of the
signal-transduction machinery to specific sub-cellular
locations to respond to environmental changes rapidly.
The C-terminal region of paxillin contains four LIM
domains which target paxillin to focal adhesions,
presumably through a direct association with the
cytoplasmic tail of beta-integrin. The N-terminal of
paxillin is leucine-rich LD-motifs. Paxillin is found
at the interface between the plasma membrane and the
actin cytoskeleton. The binding partners of paxillin
are diverse and include protein tyrosine kinases, such
as Src and FAK, structural proteins, such as vinculin
and actopaxin, and regulators of actin organization.
Paxillin recruits these proteins to their function
sites to control the dynamic changes in cell adhesion,
cytoskeletal reorganization and gene expression. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight cons erved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 54
Score = 26.5 bits (58), Expect = 2.0
Identities = 12/34 (35%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 28 WHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
WH C C + + F RDG+ YC++DY
Sbjct: 21 WHPEHFVCTHCQEEIGSR-NFFERDGQPYCEKDY 53
>gnl|CDD|188718 cd09332, LIM2_PINCH, The second LIM domain of protein PINCH. The
second LIM domain of protein PINCH: PINCH plays a
pivotal role in the assembly of focal adhesions (FAs),
regulating diverse functions in cell adhesion, growth,
and differentiation through LIM-mediated protein-protein
interactions. PINCH comprises an array of five LIM
domains that interact with integrin-linked kinase (ILK),
Nck2 (also called Nckbeta or Grb4) and other interaction
partners. These interactions are essential for
triggering the FA assembly and for relaying diverse
mechanical and biochemical signals between
Cell-extracellular matrix and the actin cytoskeleton.
LIM domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 52
Score = 26.1 bits (58), Expect = 2.7
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 110 VMRAKNKIYHVQCFCCVVCGKQL 132
V++A N +H CF C +C K+L
Sbjct: 12 VIKAMNNNWHPDCFRCEICNKEL 34
>gnl|CDD|188870 cd09486, LIM_Eplin_like_1, a LIM domain subfamily on a group of
proteins with unknown function. This model represents a
LIM domain subfamily of Eplin-like family. This family
shows highest homology to the LIM domains on Eplin and
XIRP2 protein families. Epithelial Protein Lost in
Neoplasm is a cytoskeleton-associated tumor suppressor
whose expression inversely correlates with cell growth,
motility, invasion and cancer mortality. Xirp2 is
expressed in muscles and is an important effector of the
Ang II signaling pathway in the heart. As in other LIM
domains, this domain family is 50-60 amino acids in size
and shares two characteristic zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 53
Score = 26.1 bits (57), Expect = 2.9
Identities = 12/36 (33%), Positives = 17/36 (47%), Gaps = 1/36 (2%)
Query: 113 AKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCK 148
A ++H CFCC C +L G +A +CK
Sbjct: 16 ADKLVFHNSCFCCKHCNAKLSLG-SYAALHGEFYCK 50
>gnl|CDD|188728 cd09342, LIM3_Testin_like, The third LIM domain of Testin-like
family. The third LIM domain of Testin_like family:
This family includes testin, prickle, dyxin and
LIMPETin. Structurally, testin and prickle proteins
contain three LIM domains at C-terminal; LIMPETin has
six LIM domains; and dyxin presents only two LIM
domains. However, all members of the family contain a
PET protein-protein interaction domain. Testin is a
cytoskeleton associated focal adhesion protein that
localizes along actin stress fibers, at
cell-cell-contact areas, and at focal adhesion plaques.
Testin interacts with a variety of cytoskeletal
proteins, including zyxin, mena, VASP, talin, and actin
and it is involved in cell motility and adhesion events.
Prickles have been implicated in roles of regulating
tissue polarity or planar cell polarity (PCP). Dyxin
involves in lung and heart development by interaction
with GATA6 and blocking GATA6 activated target genes.
LIMPETin might be the recombinant product of genes
coding testin and four and half LIM proteins and its
function is not well understood. As in other LIM
domains, this domain family is 50-60 amino acids in size
and shares two characteristic zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 57
Score = 25.8 bits (57), Expect = 3.1
Identities = 11/27 (40%), Positives = 15/27 (55%), Gaps = 1/27 (3%)
Query: 121 QCFCCVVCGKQLVPGDEFALREDGLFC 147
+CFCC C K L+ G F + +FC
Sbjct: 27 ECFCCSNCKKSLL-GQPFLPKNGQIFC 52
>gnl|CDD|188844 cd09460, LIM3_ZASP_Cypher, The third LIM domain of ZASP/Cypher
family. The third LIM domain of ZASP/Cypher family:
ZASP was identified in human heart and skeletal muscle
and Cypher is a mice ortholog of ZASP. ZASP/Cyppher
contains three LIM domains at the C-terminus and a PDZ
domain at N-terminus. ZASP/Cypher is required for
maintenance of Z-line structure during muscle
contraction, but not required for Z-line assembly. In
heart, Cypher/ZASP plays a structural role through its
interaction with cytoskeletal Z-line proteins. In
addition, there is increasing evidence that Cypher/ZASP
also performs signaling functions. Studies reveal that
Cypher/ZASP interacts with and directs PKC to the
Z-line, where PKC phosphorylates downstream signaling
targets. LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 55
Score = 26.2 bits (57), Expect = 3.2
Identities = 16/52 (30%), Positives = 22/52 (42%), Gaps = 1/52 (1%)
Query: 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCK 148
C C+ + D + A +H CF C VC L G F ++D CK
Sbjct: 1 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNL-EGQPFYSKKDKPLCK 51
>gnl|CDD|188780 cd09394, LIM1_Rga, The first LIM domain of Rga GTPase-Activating
Proteins. The first LIM domain of Rga
GTPase-Activating Proteins: The members of this family
contain two tandem repeats of LIM domains and a
Rho-type GTPase activating protein (RhoGap) domain. Rga
activates GTPases during polarized morphogenesis. In
yeast, a known regulating target of Rga is CDC42p, a
small GTPase. The LIM domain is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein.
Length = 55
Score = 25.8 bits (57), Expect = 3.5
Identities = 12/37 (32%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLD 43
CVGC I + + + D WH C +C +C + L
Sbjct: 1 CVGCKESITEGHAYELGGDR-WHIHCFKCYKCDKKLS 36
>gnl|CDD|193533 cd05657, M42_glucanase_like, M42 Peptidase, Endoglucanase-like
subfamily. Peptidase M42 family, glucanase (endo-1
4-beta-glucanase or endoglucanase)-like subfamily.
Proteins in this subfamily are co-catalytic
metallopeptidases, found in archaea and bacteria. They
show similarity to cellulase and endo-1,4-beta-glucanase
(endoglucanase) which typically bind two zinc or cobalt
atoms. Some of the enzymes exhibit typical
aminopeptidase specificity, whereas others are also
capable of N-terminal deblocking activity, i.e.
hydrolyzing acylated N-terminal residues. Many of these
enzymes are assembled either as tetrahedral dodecamers
or as octahedral tetracosameric structures, with the
active site located on the inside such that substrate
sizes are limited, indicating function as possible
peptide scavengers.
Length = 336
Score = 27.9 bits (63), Expect = 3.8
Identities = 9/13 (69%), Positives = 9/13 (69%)
Query: 44 ENCTCFVRDGKTY 56
ENCT RDGK Y
Sbjct: 96 ENCTIHTRDGKVY 108
Score = 27.9 bits (63), Expect = 3.8
Identities = 9/13 (69%), Positives = 9/13 (69%)
Query: 72 ENCTCFVRDGKTY 84
ENCT RDGK Y
Sbjct: 96 ENCTIHTRDGKVY 108
>gnl|CDD|236630 PRK09853, PRK09853, putative selenate reductase subunit YgfK;
Provisional.
Length = 1019
Score = 28.0 bits (63), Expect = 3.8
Identities = 18/64 (28%), Positives = 27/64 (42%), Gaps = 16/64 (25%)
Query: 30 AACLRCAECHQFLDENCTCFVRDGKTY--------CKRDYVSSEKNQFLDENCTCFVR-D 80
A C C C QF C +GK Y + D+ +S FL E+ VR +
Sbjct: 926 AMCNECGNCAQF------C-PWNGKPYKDKITLFSLEEDFENSTNPGFLVEDGRVRVRLN 978
Query: 81 GKTY 84
G+++
Sbjct: 979 GQSW 982
>gnl|CDD|176412 cd01817, RGS12_RBD, Ubiquitin domain of RGS12 and RGS14. RGS12
(regulator of G signalling 12), and RGS14, are members
of a family of GTPase-activating proteins (GAP's)
specific for the G-alpha subunit, which act as key
inhibitors of G-protein-mediated cell responses in
eukaryotes. Their domain architecture includes tandem
RBD domains as well as PDZ , PTB, and RGS, and GoLoco
domains.
Length = 73
Score = 26.2 bits (58), Expect = 4.0
Identities = 8/37 (21%), Positives = 17/37 (45%)
Query: 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLV 133
CEK +N+ D + +K + V+ G+++
Sbjct: 30 CEKRGINYAAVDLFLVGGDKPLVLDQDSSVLAGQEVR 66
>gnl|CDD|240427 PTZ00470, PTZ00470, glycoside hydrolase family 47 protein;
Provisional.
Length = 522
Score = 27.8 bits (62), Expect = 4.1
Identities = 8/30 (26%), Positives = 16/30 (53%)
Query: 155 DKSSNGENNNNNTNINNNLHNLNNEGSNSG 184
++ +N NNN N NN +++ N + +
Sbjct: 10 VHNNADDNYNNNNNNNNQINSNNPNNNGNN 39
Score = 27.0 bits (60), Expect = 6.5
Identities = 12/34 (35%), Positives = 17/34 (50%)
Query: 149 DDHEGMDKSSNGENNNNNTNINNNLHNLNNEGSN 182
H D + N NNNNN +NN +N N ++
Sbjct: 9 SVHNNADDNYNNNNNNNNQINSNNPNNNGNNQAS 42
>gnl|CDD|218851 pfam06007, PhnJ, Phosphonate metabolism protein PhnJ. This family
consists of several bacterial phosphonate metabolism
(PhnJ) sequences. The exact role that PhnJ plays in
phosphonate utilisation is unknown.
Length = 279
Score = 27.6 bits (62), Expect = 4.2
Identities = 6/17 (35%), Positives = 7/17 (41%)
Query: 28 WHAACLRCAECHQFLDE 44
+ C C FLDE
Sbjct: 235 FDDPCALCGSTDSFLDE 251
>gnl|CDD|232844 TIGR00143, hypF, [NiFe] hydrogenase maturation protein HypF. A
previously described regulatory effect of HypF
mutatation is attributable to loss of activity of a
regulatory hydrogenase. A zinc finger-like region
CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported
the regulatory hypothesis. However, more recent work
(PUBMED:11375153) shows the direct effect is on the
activity of expressed hydrogenases with nickel/iron
centers, rather than on expression [Protein fate,
Protein modification and repair].
Length = 711
Score = 27.8 bits (62), Expect = 4.2
Identities = 17/75 (22%), Positives = 24/75 (32%), Gaps = 24/75 (32%)
Query: 95 TKCEKCN--------LNFKREDFVMRA--------------KNKIYHVQCFCCVVCGKQL 132
C C L + RE+ M ++ +H Q C CG QL
Sbjct: 91 ISCTHCGPRFTIIEALPYDRENTSMADFPLCPDCAKEYKDPLDRRFHAQPIACPRCGPQL 150
Query: 133 --VPGDEFALREDGL 145
V A ++D L
Sbjct: 151 NFVSRGGHAEQDDAL 165
>gnl|CDD|188869 cd09485, LIM_Eplin_alpha_beta, The Lim domain of Epithelial Protein
Lost in Neoplasm (Eplin). The Lim domain of Epithelial
Protein Lost in Neoplasm (Eplin): Epithelial Protein
Lost in Neoplasm is a cytoskeleton-associated tumor
suppressor whose expression inversely correlates with
cell growth, motility, invasion and cancer mortality.
Eplin interacts and stabilizes F-actin filaments and
stress fibers, which correlates with its ability to
suppress anchorage independent growth. In epithelial
cells, Eplin is required for formation of the F-actin
adhesion belt by binding to the E-cadherin-catenin
complex through alpha-catenin. Eplin is expressed in two
isoforms, a longer Eplin-beta and a shorter Eplin-alpha.
Eplin-alpha mRNA is detected in various tissues and cell
lines, but is absent or down regulated in cancer cells.
As in other LIM domains, this domain family is 50-60
amino acids in size and shares two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 53
Score = 25.6 bits (56), Expect = 4.6
Identities = 13/36 (36%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 113 AKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCK 148
A +IYH CF C C +L G +A ++CK
Sbjct: 16 ANQQIYHNSCFRCSYCNTKLSLGT-YASLHGNIYCK 50
>gnl|CDD|188781 cd09395, LIM2_Rga, The second LIM domain of Rga
GTPase-Activating Proteins. The second LIM domain of
Rga GTPase-Activating Proteins: The members of this
family contain two tandem repeats of LIM domains and a
Rho-type GTPase activating protein (RhoGap) domain. Rga
activates GTPases during polarized morphogenesis. In
yeast, a known regulating target of Rga is CDC42p, a
small GTPase. The LIM domain is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein.
Length = 53
Score = 25.5 bits (56), Expect = 4.8
Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECH 39
C CG +I D IL + D + + C RC C
Sbjct: 1 CKNCGKKIDDTAILL-SSDEAYCSDCFRCRRCS 32
>gnl|CDD|188861 cd09477, LIM2_TLP, The second LIM domain of thymus LIM protein
(TLP). The second LIM domain of thymus LIM protein
(TLP): TLP is the distant member of the CRP family of
proteins. TLP has two isomers (TLP-A and TLP-B) and
sharing approximately 30% with each of the three other
CRPs. Like CRP1, CRP2 and CRP3/MLP, TLP has two LIM
domains, connected by a flexible linker region. Unlike
the CRPs, TLP lacks the nuclear targeting signal
(K/R-K/R-Y-G-P-K) and is localized solely in the
cytoplasm. TLP is specifically expressed in the thymus
in a subset of cortical epithelial cells. TLP has a
role in development of normal thymus and in controlling
the development and differentiation of thymic
epithelial cells. LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 54
Score = 25.4 bits (55), Expect = 5.4
Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 4/52 (7%)
Query: 7 CVGCGGQIH-DQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYC 57
C GCG ++ + ++ + + WH CLRC C + L DG YC
Sbjct: 1 CPGCGKPVYFAEKVMSLGRN--WHRPCLRCQRCKKTLTAGGHA-EHDGSPYC 49
>gnl|CDD|177395 PHA02565, 49, recombination endonuclease VII; Provisional.
Length = 157
Score = 26.6 bits (59), Expect = 5.5
Identities = 6/22 (27%), Positives = 11/22 (50%)
Query: 113 AKNKIYHVQCFCCVVCGKQLVP 134
K K++ Q C +C ++L
Sbjct: 11 EKQKLFEAQNGICPLCKRELDG 32
>gnl|CDD|188779 cd09393, LIM3_Lrg1p_like, The third LIM domain of Lrg1p, a LIM
and RhoGap domain containing protein. The third LIM
domain of Lrg1p, a LIM and RhoGap domain containing
protein: The members of this family contain three
tandem repeats of LIM domains and a Rho-type GTPase
activating protein (RhoGap) domain. Lrg1p is a Rho1
GTPase-activating protein required for efficient cell
fusion in yeast. Lrg1p-GAP domain strongly and
specifically stimulates the GTPase activity of Rho1p, a
regulator of beta (1-3)-glucan synthase in vitro. The
LIM domain is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein.
Length = 56
Score = 25.4 bits (56), Expect = 5.6
Identities = 8/35 (22%), Positives = 14/35 (40%), Gaps = 3/35 (8%)
Query: 28 WHAACLRCAECHQFLD---ENCTCFVRDGKTYCKR 59
WH C C+ CH+ + + +D + C
Sbjct: 20 WHLKCFTCSRCHREISSELSDAAFNNKDQRILCSN 54
>gnl|CDD|218272 pfam04797, Herpes_ORF11, Herpesvirus dUTPase protein. This family
of proteins are found in Herpesvirus proteins. This
family includes proteins called ORF10 and ORF11 amongst
others. However, these proteins seem to be related to
other dUTPases pfam00692 suggesting that these proteins
are also dUTPases (Bateman A pers. obs.).
Length = 374
Score = 26.9 bits (60), Expect = 6.9
Identities = 15/66 (22%), Positives = 20/66 (30%), Gaps = 5/66 (7%)
Query: 43 DENCTCFVRDGKTYC--KRDYVSSEKNQFLDENCTC-FVRDGKTYCKRDYVRLFGTKCEK 99
E T + KT KR + + E C VR GK Y + K E
Sbjct: 165 PETYTPYFLAQKTKPFLKRGFARL--HAEEGEVCPVNAVRLGKNYVRVSVTLPSEAKSET 222
Query: 100 CNLNFK 105
+
Sbjct: 223 VLVKVP 228
>gnl|CDD|236304 PRK08581, PRK08581, N-acetylmuramoyl-L-alanine amidase; Validated.
Length = 619
Score = 27.1 bits (60), Expect = 7.4
Identities = 7/38 (18%), Positives = 17/38 (44%)
Query: 149 DDHEGMDKSSNGENNNNNTNINNNLHNLNNEGSNSGKI 186
D+E S N++N + ++ ++ + + S K
Sbjct: 134 SDYEQPRNSEKSTNDSNKNSDSSIKNDTDTQSSKQDKA 171
>gnl|CDD|188826 cd09442, LIM_Eplin_like, The Lim domain of Epithelial Protein Lost
in Neoplasm (Eplin) like proteins. The Lim domain of
Epithelial Protein Lost in Neoplasm (Eplin) like
proteins: This family contains Epithelial Protein Lost
in Neoplasm in Neoplasm (Eplin), xin actin-binding
repeat-containing protein 2 (XIRP2) and a group of
protein with unknown function. The members of this
family all contain a single LIM domain. Epithelial
Protein Lost in Neoplasm is a cytoskeleton-associated
tumor suppressor whose expression inversely correlates
with cell growth, motility, invasion and cancer
mortality. Eplin interacts and stabilizes F-actin
filaments and stress fibers, which correlates with its
ability to suppress anchorage independent growth. In
epithelial cells, Eplin is required for formation of the
F-actin adhesion belt by binding to the
E-cadherin-catenin complex through alpha-catenin. Eplin
is expressed in two isoforms, a longer Eplin-beta and a
shorter Eplin-alpha. Eplin-alpha mRNA is detected in
various tissues and cell lines, but is absent or down
regulated in cancer cells. Xirp2 contains a LIM domain
and Xin re peats for binding to and stabilising F-actin.
Xirp2 is expressed in muscles and is significantly
induced in the heart in response to systemic
administration of angiotensin II. Xirp2 is an important
effector of the Ang II signaling pathway in the heart.
The expression of Xirp2 is activated by myocyte enhancer
factor (MEF)2A, whose transcriptional activity is
stimulated by angiotersin II. Thus, Xirp2 plays
important pathological roles in the angiotensin II
induced hypertension. As in other LIM domains, this
domain family is 50-60 amino acids in size and shares
two characteristic zinc finger motifs. The two zinc
fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 53
Score = 24.7 bits (54), Expect = 7.4
Identities = 9/28 (32%), Positives = 14/28 (50%)
Query: 113 AKNKIYHVQCFCCVVCGKQLVPGDEFAL 140
A + +H CF C C +L G+ +L
Sbjct: 16 ADKQNFHKSCFRCEHCNSKLSLGNYASL 43
>gnl|CDD|188733 cd09347, LIM4_FHL, The fourth LIM domain of Four and a half LIM
domains protein (FHL). The fourth LIM domain of Four
and a half LIM domains protein (FHL): LIM-only protein
family consists of five members, designated FHL1, FHL2,
FHL3, FHL5 and LIMPETin. The first four members are
composed of four complete LIM domains arranged in tandem
and an N-terminal single zinc finger domain with a
consensus sequence equivalent to the C-terminal half of
a LIM domain. LIMPETin is an exception, containing six
LIM domains. FHL1, 2 and 3 are predominantly expressed
in muscle tissues, and FHL5 is highly expressed in male
germ cells. FHL proteins exert their roles as
transcription co-activators or co-repressors through a
wide array of interaction partners. For example, FHL1
binds to Myosin-binding protein C, regulating myosin
filament formation and sarcomere assembly. FHL2 has
shown to interact with more than 50 different proteins,
including receptors, structural proteins, transcription
factors and cofactors, signal transducers, splicing
factors, DNA replication and repair enzymes, and
metabolic enzymes. FHL3 interacts with many
transcription factors, such as CREB, BKLF/KLF3, CtBP2,
MyoD, and MZF_1. FHL5 is a tissue-specific coactivator
of CREB/CREM family transcription factors. LIM domains
are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 56
Score = 25.0 bits (55), Expect = 7.7
Identities = 11/32 (34%), Positives = 15/32 (46%), Gaps = 1/32 (3%)
Query: 118 YHVQCFCCVVCGKQLVPGDEFALREDGLFCKD 149
+H CF C C LV G F + D + C +
Sbjct: 24 WHSDCFNCGKCSVSLV-GQGFLTQRDEILCPE 54
>gnl|CDD|188842 cd09458, LIM3_Enigma, The third LIM domain of Enigma. The third
LIM domain of Enigma: Enigma was initially characterized
in humans as a protein containing three LIM domains at
the C-terminus and a PDZ domain at N-terminus. The
third LIM domain specifically interacts with the insulin
receptor and the second LIM domain interacts with the
receptor tyrosine kinase Ret and the adaptor protein
APS. Thus Enigma is implicated in signal transduction
processes such as mitogenic activity, insulin related
actin organization, and glucose metabolism. Enigma is
expressed in multiple tissues, such as skeletal muscle,
heart, bone, and brain. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 55
Score = 25.0 bits (54), Expect = 7.9
Identities = 15/52 (28%), Positives = 21/52 (40%), Gaps = 1/52 (1%)
Query: 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCK 148
C C+ D + A +H CF C +C L G F ++D CK
Sbjct: 1 CHGCDFKIDAGDRFLEALGFSWHDTCFVCAICQINL-EGKTFYSKKDKPLCK 51
>gnl|CDD|188862 cd09478, LIM_CRIP, The LIM domain of Cysteine-Rich Intestinal
Protein (CRIP). The LIM domain of Cysteine-Rich
Intestinal Protein (CRIP): CRIP is a short protein with
only one LIM domain. CRIP gene is developmentally
regulated and can be induced by glucocorticoid hormones
during the first three postnatal weeks. The domain
shows close sequence homology to LIM domain of thymus
LIM protein. However, unlike the TLP proteins which
have two LIM domains, the members of this family have
only one LIM domain. LIM domains are 50-60 amino acids
in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 54
Score = 24.8 bits (54), Expect = 8.0
Identities = 12/31 (38%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 27 EWHAACLRCAECHQFLDENCTCFVRDGKTYC 57
+WH CL+C +C + L DGK YC
Sbjct: 20 DWHRPCLKCEKCGKTLTPGSHA-EHDGKPYC 49
>gnl|CDD|237510 PRK13795, PRK13795, hypothetical protein; Provisional.
Length = 636
Score = 26.9 bits (60), Expect = 8.2
Identities = 14/46 (30%), Positives = 22/46 (47%), Gaps = 12/46 (26%)
Query: 2 RRLSLCVGCG--------GQIH-DQYILRVAPDLEWHAACLRCAEC 38
RR + CVGCG G I ++ +++ D E C+ C +C
Sbjct: 578 RRAAECVGCGVCVGACPTGAIRIEEGKRKISVDEE---KCIHCGKC 620
>gnl|CDD|188815 cd09431, LIM3_Fhl2, The third LIM domain of Four and a half LIM
domains protein 2 (FHL2). The third LIM domain of Four
and a half LIM domains protein 2 (FHL2): FHL2 is one of
the best studied FHL proteins. FHL2 expression is most
abundant in the heart, and in brain, liver and lung to a
lesser extent. FHL2 participates in a wide range of
cellular processes, such as transcriptional regulation,
signal transduction, and cell survival by binding to
various protein partners. FHL2 has shown to interact
with more than 50 different proteins, including
receptors, structural proteins, transcription factors
and cofactors, signal transducers, splicing factors, DNA
replication and repair enzymes, and metabolic enzymes.
Although FHL2 is abundantly expressed in heart, the fhl2
null mice are viable and had no detectable abnormal
cardiac phenotype. LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to s upport the assembly of multimeric protein
complexes.
Length = 57
Score = 25.0 bits (54), Expect = 8.8
Identities = 13/34 (38%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 114 KNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFC 147
+++ +H +CF C C KQL G F R+D +C
Sbjct: 16 RDQPWHKECFVCTGCKKQL-SGQRFTSRDDFAYC 48
>gnl|CDD|223146 COG0068, HypF, Hydrogenase maturation factor [Posttranslational
modification, protein turnover, chaperones].
Length = 750
Score = 26.6 bits (59), Expect = 9.9
Identities = 10/36 (27%), Positives = 14/36 (38%), Gaps = 6/36 (16%)
Query: 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQL 132
C C+ +K N+ +H Q C CG L
Sbjct: 154 CPFCDKEYKD------PLNRRFHAQPIACPKCGPHL 183
>gnl|CDD|188746 cd09360, LIM_ALP_like, The LIM domain of ALP (actinin-associated
LIM protein) family. This family represents the LIM
domain of ALP (actinin-associated LIM protein) family.
Four proteins: ALP, CLP36, RIL, and Mystique have been
classified into the ALP subfamily of LIM domain
proteins. Each member of the subfamily contains an
N-terminal PDZ domain and a C-terminal LIM domain.
Functionally, these proteins bind to alpha-actinin
through their PDZ domains and bind or other signaling
molecules through their LIM domains. ALP proteins have
been implicated in cardiac and skeletal muscle
structure, function and disease, platelet, and
epithelial cell motility. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 52
Score = 24.3 bits (53), Expect = 10.0
Identities = 13/36 (36%), Positives = 19/36 (52%), Gaps = 2/36 (5%)
Query: 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQL 132
C+KC V++A++K H +CF C CG L
Sbjct: 1 CDKCGNGIV--GVVVKARDKNRHPECFVCADCGLNL 34
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.324 0.140 0.463
Gapped
Lambda K H
0.267 0.0729 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,230,358
Number of extensions: 799206
Number of successful extensions: 1628
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1532
Number of HSP's successfully gapped: 307
Length of query: 191
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 100
Effective length of database: 6,901,388
Effective search space: 690138800
Effective search space used: 690138800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 56 (25.3 bits)